I see two questions here. The first is why self-inductance is not considered when solving Faraday's law problems, and the second is why an EMF can ever produce a current in a circuit with non-zero self-inductance. I will answer both of these in turn.
1. Why self-inductance is not considered when solving Faraday's law problems
Self inductance should be considered, but is left out for simplicity. So for example, if you have a planar circuit with inductance $L$, resistance $R$, area $A$, and there is a magnetic field of strength $B$ normal to the plane of the circuit, then the EMF is given by $\mathcal{E}=-L \dot{I} - A \dot{B}$.
This means, for example, that if $\dot{B}$ is constant, then, setting $IR=\mathcal{E}$, we find $\dot{I} = -\frac{R}{L} I - \frac{A}{L} \dot{B}$. If the current is $0$ at $t=0$, then for $t>0$ the current is given by $I(t)=-\frac{A}{R} \dot{B} \left(1-\exp(\frac{-t}{L/R}) \right)$. At very late times $t \gg \frac{L}{R}$, the current is $-\frac{A \dot{B}}{R}$, as you would find by ignoring the inductance. However, at early times, the inductance prevents a sudden jump of the current to this value, so there is a factor of $1-\exp(\frac{-t}{L/R})$, which causes a smooth increase in the current.
2. Why an EMF can ever produce a current in a circuit with non-zero self-inductance.
You are worried that EMF caused by the circuit's inductance will prevent any current from flowing. Consider the planar circuit as in part one, and suppose there is a external emf $V$ applied to the circuit (and no longer any external magnetic field). The easiest way to see that current will flow is by making an analogy with classical mechanics: the current $I$ is analogous to a velocty $v$; the resistance is analogous to a drag term, since it represents dissipation; the inductance is like mass, since the inductance opposes a change in the current the same way a mass opposes a change in velocity; and the EMF $V$ is analogous to a force. Now you have no problem believing that if you push on an object in a viscous fluid it will start moving, so you should have no problem believing that a current will start to flow.
To analyze the math, all we have to do is replace $-A \dot{B}$ by $V$ in our previous equations, we find the current is $I(t) = \frac{V}{R} \left(1-\exp(\frac{-t}{L/R}) \right)$, so as before the current increases smoothly from $0$ to its value $\frac{V}{R}$ at $t=\infty$.
Here is one way to think about it:
When a charged particle travels in a magnetic field, it experiences a force. If the particle is stationary but the field is moving, then in the frame of reference of the field the particle should see the same force.
Now let's take a conductor wound into a coil. In order to increase the magnetic field inside, I could take a dipole magnet and move it close to the coil. As I do so, magnetic field lines cross the conductor, and generate a force on the charge carriers.
It is a convenient trick for figuring out "what goes where" to know that the induced current will flow so as to oppose the magnetic field change that generated it. In the perfect case of a superconductor, this "opposing" is perfect - this is the basis of magnetic levitation. For resistive conductors, the induced current is not quite sufficient to oppose the magnetic field, so some magnetic field is left.
The point is that the flowing of the current is instantaneous - it happens as the magnetic field tries to establish in the coil. So it's not "Apply field in coil. Coil notices, and generates an opposing field. " - instead, it is "Start to apply field in coil. Coil notices and prevents field getting to expected strength".
Not sure if this makes things any clearer...
Best Answer
This comes from Maxwell's equations. Start with Faraday's Law:
$$ \nabla \times E = -\frac{\partial B}{\partial t}$$
Note the negative sign. If we integrate both sides by the area through which there is a magnetic field (think of the cross-section of a solenoid, for example), then we get:
$$ \int (\nabla \times E) \cdot dA = \oint E\cdot dl = - \frac{\partial \Phi}{\partial t}$$
The middle term follows from applying Stoke's theorem on the first term. The middle term is also the definition of voltage. The final definition is flux ($\Phi$) which is the product of the magnetic field and the cross-sectional area the field passes through, which is how one arrives at the third term.
The 'opposite V' or back EMF acts to stabilize the current flowing. Suppose you increase V, and hence A, which increases the flux and hence slowly increases the back EMF. Then suppose that you stop increasing V. The back EMF will persist and slowly decay thereafter until the current stops changing (current reaches steady-state). If you were to instead keep increasing V, you'd keep increasing A, keep increasing the flux and keep increasing the back EMF (it would exacerbate the situation).