As a theoretical physicist who shifted to pure mathematics, I think to answer this question and as a clarification to previous posts, we should not forget the historical side of the evolution and origins of the terms involved in physics theory modeling.
The origin of the principle of stationary ('least' most of the time) action comes as a variational formulation using a functional $S[q(t)]:=\int_{t_1}^{t_2}L(q^i (t),\dot{q}^i (t);t)dt$ for the Lagrange equations of the real motion of a system with generalized coordinates $q^i (t)$ (obtained this way they are called Euler-Lagrange equations):
$$\delta S[q_{real}(t)]=0\Rightarrow \frac{d}{dt}\frac{\partial L}{\partial \dot{q}^i}-\frac{\partial L}{\partial q^i}=0$$
The original Lagrange equations of motion were obtained as a reformulation of Newton's second law of mechanics for the case of generalized coordinates (the remaining degrees of freedom after introducing constraints) as an easier to handle version of D'Alembert's principle. D'Alembert wrote the 'virtal work' principle as a way to state a general equation for statics, which in a way amounts to postulate that constraint forces do not exert work (as they should be internal and the weak 3rd law applies). Now given Newton's second law for a system of particles, D'Alembert reformulates constrained dynamics as statics introducing the inertial force (you can see details at wikipedia) $$\sum_i (\vec{F}_{i}^{ext}-\frac{d\vec{p}_i}{dt})\cdot\delta \vec{r_i}=0$$
Lagrange wanted to work only with generalized coordinates which changing variables in D'Alembert's principle led him to the original Lagrange's equations of motion in terms of a kinetic generalised energy $T$ and generalized forces $Q_i$; furthermore he absorbed those conservative forces which derived from a potential $Q_i^c=-\partial U/\partial q_i$ (or more generally those which even depended on speed or time but had the required form of the left-hand side) along with the kinetic energy, into a function $L=T-U$ now called the Lagrangian $$\frac{d}{dt}\frac{\partial T}{\partial \dot{q}^i}-\frac{\partial T}{\partial q^i}=Q_i\Rightarrow \frac{d}{dt}\frac{\partial L}{\partial \dot{q}^i}-\frac{\partial L}{\partial q^i}=Q_i^{no-c.}$$
That is the origin of the form of the lagrangian as $L=T-U$. Now, the non-conservative forces $Q_i^{no-c.}$ appear because we are considering general 'open systems' which interchange energy with their enviroment, other systems as sources of energy, etc. To check this form in detail, first consdier that a closed system is always of the form $L=T-U$ because of a constructive reasoning as follows. For a free particle, at least locally, because of the homogeneity of space and time, and isotropy of space, we must have $L(q_i,\dot{q}_i;t)=T(v^2)$, that is a scalar which only depends on the particle and its speed (but no direction); since a free particle must still be free in another inertial system by def. the relation must be linear $L=a\cdot v^2$ (this is because any other Lagrangian giving the same equations of motion has to be of the form $L'=A\cdot L+\frac{d}{dt}\Omega(q;t)$ for which an inertial transformation $\vec{v}'=\vec{v}-\vec{\epsilon}$ must imply at first order $-2\vec{v}\cdot\vec{\epsilon}\partial L(v^2)/\partial (v^2)\propto d\Omega(q;t)/dt\Leftrightarrow \partial L/\partial (v^2)=0$); now the constant $a$ characterizes the particle, and must reduce to the free Newtonian second law ($p_i=m\cdot v_i =0$) therefore $a=m/2$. For a system of free particles without interactions the same applies summing over the individual kinetic energies $L_{free}=T=\frac{1}{2}\sum_i m_i v_i^2=\frac{1}{2}\sum_{i,j} A_{ij}\dot{q}^i\dot{q}^j$ (when $T$ is a cuadratic form the system is called 'natural' which happens when $\partial \vec{r}_k(q^i(t),\dot{q}^i(t);t)/\partial t = 0$ for all particles $k$, common for the natural case of constraints not dependent on time). To add interactions between particles in a closed system, their degrees of freedom must be coupled, which just means that the relative energies are not lost to the exterior, and this is satisfactorily implemented by a potential function $U=U(q_i,\dot{q}_i)$. By this method we obtain a general framework for mechanics using Lagrange's equations: postulating different potentials we obtain different models of interactions which shall be contrasted with experiment to constrain the form of $U$ (this may be done to obtain just effective phenomenological models, nevertheless all fundamental interactions of physics seem to fit this framework very well). Finally, when part B of the system A+B is fixed (like considered external) its motion can be treated like already 'solved', which opens the previous closed system, separating some of the degrees of freedom $q_B^i(t)$; therefore the Lagrangian decouples $L_{open}=T_A+T_B(\dot{q}^i_B(t))-U(q_A,q_B(t),\dot{q}_A,\dot{q}_B(t))$, in this case $T_B=d\Omega(q_B,t)/dt$ for some $\Omega$, so we can neglect that part since does not contribute to the equations of motion and therefore $L_{open}=T_A-U_{open}(q_A,\dot{q}_A,t)$. This way $U$ creates the effect of non-conservative forces which are just those that add or subtract energy from the system without taking into account where this energy goes.
Therefore we can consider the Lagrange equation (without non-conservative forces) as the general more fundamental equation given individual interactions between the particles of the Universe, at least in principle. This is why the form $L=T-U$ is the usual approach in theoretical physics to deal with dynamics, since the very concept of instantaneous force at a distance à-la Newton is anti-natural (above all after special-general relativity) and the energetic local approach is not only mathematically better but philosophically more satisfactory. The Hamiltonian approach can be taken also as a starting point, or as a Legendre transformation of Lagrange dynamics, but that way one makes a non-relativistic break down of the coordinates $x^i, t$ which is useful for non-relativistic quantum mechanics.
Now in general, physics is a theory of fields so we want to add these to the framework. This is easily done by considering them as continuous systems of degrees of freedom, providing generalizations of kinetic and potential energies of those.
Furthermore one wishes for a (special or general) relativistic invariant theory which forces the $Ldt$ to be a Lorentz scalar in order to get Lorentz-covariant ($SO(3,1)$) equations of motion (i.e. covariant as tensor equations in a pseudo-Riemannian manifold). This way the free case reasoned above leads us to $ds=Ldt$ (where $ds$ is the relativistic space-time interval or 'proper time' measured by the particle) which indeed reduces to $ds\approx \frac{1}{2}mv^2$ for speeds $v\ll c$, and therefore can be taken as a relativistic generalization of the framework. Nevertheless point-particles are idealizations and both the classical and quantum theories require a field-theoretic treatment of matter (in the classical case, particles appear as small density lumps, and in the quantum case particle behaviour arises for discrete-like energy levels of the quantum field states). In the wikipedia article about Lagrangians different examples can be seen from point particles to fields, their kinetic terms and so on.
In any case, the traditional form $L=T-U$ has its roots in the very nature of mechanics and any modern field theory is created by building up possible $T-U$ functionals from the field's degrees of freedom, i.e. the fields $\phi_a(x^\mu)$ and their "velocities" $\partial \phi_a/\partial x^\nu$ (for relativistic invariance reasons time-like speed $\frac{\partial}{\partial t}$ is not enough and the whole $\partial_\nu$ must be used). Hence one constructs kinetic terms like (Einstein's summation convenction) $T_\phi=\frac{1}{2}\partial_\mu\phi_a\partial^\mu\phi_a$ for scalar fields or $T_A=F_{\mu\nu}F^{\mu\nu}$ for vector fields ($F_{\mu\nu}:=\partial_\mu A_\nu-\partial_\nu A_\mu$ is in this case the tensor constructed from the field used to define its kinetic energy because we want to build invariant 'speed-like' $\partial_\mu$ scalars that are as well Gauge invariant which is another physical symmetry typically required besides Lorentz; furthermore, requiring gauge invariance for different Lie groups, tyipcally $SU(N)$, one forces the automatic appearance of fields and couplings between the matter fields responsible for the interactions, which is just working with connections and curvatures of fiber bundles). Since any term which makes the field equation of motion non-homogeneous is considered a source of perturbation, or force, one sees the corresponding couplings in the Lagrangian like a potential energy, giving as always $\mathcal{L}=T_\phi+T_A-U(A_\mu,\phi)$. With this, the coupled physical equations of motion are deduced for the principle of stationary action, where now the integration must be over the whole space and an interval of time (i.e. $\mathcal{L}$ is a density), the field Euler-Lagrange equations of motion:
$$\partial_\mu\frac{\partial\mathcal{L}}{\partial (\partial_\mu\phi)}-\frac{\partial\mathcal{L}}{\partial\phi}=0$$
Finally these equations give the solutions of motion, that is the real field configurations at any point in space-time, which contribute the most in a quantum-theoretic framework, where one weighs complex transition amplitudes by Feynman operational methods using the action for each possible field-configuration ('motion'): $e^{\frac{i}{\hbar}S[\phi,A_\mu]}$. As remarked in other comment, the semi-classical approximation $\hbar\rightarrow 0$ makes the classical solution of Euler-Lagrange the predominant one, hence deducing the principle of stationary action. (Also, in the non-relativistic hamiltonian quantum-mechanics Ehrenfest's theorem provides a classical Newton-like equation of motion for the average degrees of freedom)
Indeed as science makes progress we must see previous theories and models as limiting cases of new more precise theories, but in the beginning any physical theory must be constructed by physical insight, intuition and permanent comparison with experiment. Even though Feynman titled his thesis that way, he does not develop his approach to quantum theory starting from the action-principle, on the contrary he works with standard (hamiltonian) quantum mechanics and obtains a novel method for computing quantum probability amplitudes in which the classical action appears. You could start with quantum mechanics as an axiomatic system, develop Feynman's approach to quantum propagators of motion and deduce that classical approximate solutions of motion must obey, at first order of quantum corrections, the classical Euler-Lagrange equations of motion. At the same time, you need the input from the experimentally succsessful classical mechanics to get to quantum mechanics... and so forth. In the end at any moment of time in the history of science we are getting better and better mathematical structures that model reality to different degrees of precision; the important point is that a new one must contain an old one as an approximation in some regime, and explain even more. This way, theoretical physics tends to get better structures to encompass more phenomena from Nature in a simpler and simpler manner as it explains more effective laws with less theories (currently almost all the phenomena observed is explained by general relativity and quantum field theory, and unifying both is the neverending quest for the holy grail of physics).
Best Answer
Mathematics is virtually the only profession that has the luxury of insisting on near-100% certainty. In physics, one is always making approximations and idealised assumptions, and even the known laws of physics may themselves only be approximations of a more accurate set of laws. In such a context, it is far more efficient to rely on heuristics that are accurate 99% of the time, than to insist on rigorous proof that is correct 100% of the time. (In principle, even a mathematically rigorous argument could be subject to scrutiny by the logicians and philosophers, but this is still a far stricter standard than what is needed for a physically convincing argument.)
A typical example of a heuristic is this: if a dynamical system has no obvious conservation laws or other structure to it that would restrict the dynamics, then it is likely to be mixing. With this heuristic one can do a huge amount of statistical mechanics; but it is completely non-rigorous. And indeed, the rigorous theory of statistical mechanics lags far behind the heuristic theory, and is thus far less useful for physics. In physics, it's OK if Maxwell's demon (or some other troublemaker) steps in to ruin everything $10^{-100}$ of the time; but this is unacceptable by the standards of rigorous mathematics.
A mathematical instance of the above heuristic in action would be the assertion that the digits of pi are uniformly distributed because there is no obvious reason why they should not be so. This is extremely convincing at the heuristic level, but falls well short of a rigorous proof, which is still completely out of reach of known methods (we can't rule out the bizarre possibility that pi has attached to it its own "Maxwell's demon").
Note though that these types of heuristics are routinely used in certain areas of mathematics, such as cryptography; and conversely there are plenty of physicists who work on rigorous mathematics; and there are people who would classify themselves as both mathematicians and physicists, or who do a mixture of rigorous and heuristic work. So the distinction is not really so sharp on closer inspection.