Imagine you live in a universe governed by extremely simple rules, like Conway's Game of Life, for example. Once you discovered those rules, you might wonder, "Why do cells come alive if they have three living neighbors? Why do they die if they have one? How does that work?" (By "how" here I am referring to "what underlying mechanism makes it work?", which is my interpretation of "how" in the original question.)
In a simulation of the Game of Life that you run on your computer, there is a good answer to this. You can examine the source code, look at the hardware of the computer, and eventually arrive at a complete description of exactly what goes on such that little squares on your computer monitor light up and go off according to the rules.
But we're imagining that these rules are just how the universe works. In that case, there may be no reason at all. Maybe it just does it, full stop.
As humans, though, I think we might find that very hard to accept. There are many cellular automata very similar to the Game of Life, but their behavior is not nearly so rich. Why did we get the one universe with the interesting laws? And how does the universe know to implement those laws without screwing up? Surely there must be some wheels and gears beneath there!
That sort of curiosity is extremely important for physicists, and it has led to a lot of new understanding. Peter Shor pointed out in the comments that wondering about how quantum mechanics works led to quantum information and computation. Famously, Einstein wondered about how electromagnetism worked, leading to understanding relativity. Frequently, a theory of physics doesn't quite feel right to us. That drives curiosity. We demand an answer, and eventually it leads to breakthroughs and new theories.
Physicists have derived great benefit from this approach of taking the pieces that don't feel right or don't feel well-enough explained and using that as a springboard to go deeper, but sometimes it also leads to complete frustration. It turns out that the universe isn't obliged to be the way we want.
If you lived in the Game of Life universe, once you figured out the rule it was following, you could keep asking forever, "Why does it have that rule? How does it implement it?" without getting anywhere. The rule itself is just a short little description. It just says that there's a grid of cells and that they light up and turn off according to a simple pattern, and that's all it says. If there was nothing deeper going on than that, oh well. We wouldn't have to give up trying to find a deeper explanation, but we aren't owed one.
My argument is that real laws of physics are the same. So in General Relativity, we posit that the Einstein equation is true. The theory of General Relativity itself makes no comment on this, just as the theory of the Game of Life makes no comment on why cells with three living neighbors come alive.
So when you ask, "How does something about the mass energy tensor alter geodesics or 4-velocity vectors? I see no explanation of gravity in GR merely a more detailed description of the motions it effects," you are right. GR doesn't say how it does it.
It could be that there's an explanation, but it doesn't seem likely to me that the fundamental problem will go away. For example, suppose someone tells you that gravitation works by sending particles called gravitons around, and gives a detailed description of the theory of gravitons. Couldn't we then ask the same question? How do the gravitons interact with spacetime? We could describe the precise mathematical rules, but fundamentally, this anthropocentric feeling of dissatisfaction would remain. Why those rules for gravitons? If they're derived from some set of appealing principles, why those principles?
Elsewhere in physics, how do wavefunctions know to obey the Schrodinger equation? What forces them to obey that equation rather than doing something else? Nothing. They just do that. It's purely a description of how the wavefunctions behave. The problem is the same, as far as I can see. (You can recast QM in some new formulation, but I don't think this averts the "problem".)
To answer your question as best I understand it, you are right that GR is just a description, nothing more. That may not always be true for GR in particular, but it seems likely to me it will always be true for something. (I can't say for sure, of course, since I don't know what the "something" will be!) It is the nature of theories of physics to be just descriptions. We don't have to accept that as a final word, and our desire to understand more deeply fuels our greatest communal quest for knowledge, but ultimately the universe will do what it will do, and can't be bullied into explaining itself just because things don't feel mechanistic enough for us.
note: This answer is completely rewritten after reading the helpful comments from Qmechanic, Peter Shor, and dmckee. Thank you for your input. This answer is essentially philosophical, so disagreement on it is inevitable, and it represents only my personal opinion.
Best Answer
1) I gather you mean gravitation potential energy of the test particle. Well, any such thing is only useful in so far as it is related to a constant of motion throughout the geodesic--in the case of gravitational potential, being part of the conserved mechanical energy, kinetic + potential. (Another example could be angular momentum.)
In GTR, these constants are given by a Killing vector field, which is an infinitesimal generator of an isometry: spacetime "looks the same" in the direction of a Killing vector. Most spacetimes do not have any, but by definition, a static spacetime has a timelike Killing vector field, and can always be put in the following form: $$ds^2 = -\lambda dt^2 + d\Sigma^2,$$ where $d\Sigma^2$ is the metric for any spacelike manifold and $\lambda$ is independent of $t$. The factor $\lambda^{1/2}$ is commonly called the gravitational redshift.
For example, for the Scwarzschild spacetime in the usual Schwarzschild coordinates, $\lambda = \left(1-\frac{2GM}{c^2R}\right)$, and the following is a constant of motion representing the specific (per-mass) energy of the freefalling particle: $$e = \left(1-\frac{2GM}{c^2r}\right)\frac{dt}{d\tau}.$$ This is the natural generalization of the total mechanical energy, including also rest-mass energy; for the Schwarzschild case, the spherical symmetry allows one to build an "effective potential" quite analogous to the Newtonian case, but that approach is less useful in general.
2) Gravitational energy cannot be explicitly included in the Einstein field equations because the equivalence principle--there is always a local inertial frame (the free-falling one) in which spacetime looks like the ordinary, flat, special-relativistic one. Hence if there was a frame-independent local notion of gravitational energy, i.e., a tensor, that tensor is zero in some local frame, and hence zero in every frame.
However, one can think of the non-linearity of the Einstein field equation as caused by gravitational energy itself interacting with spacetime. In this sense, gravitational energy is "implicitly" included. Another thing one can do is try to build another notion of gravitational energy that's not necessarily both local and frame-independent, e.g., Landau-Liftshitz pseudotensor and others.