Certainly, one can examine thermodynamics in the limited context that you describe, but it also has application related to the issue of the mechanism and the related processes. One common use of the Second Law is to determine the direction of processes. The various statements of the Second Law all have an implicit understanding of the mechanism. The mechanism can be viewed as the boundary conditions and constraints imposed on a system.
The whole thermodynamic argument is a good example how many have distorted a field based on their bias for naturalism and the evolutionary paradigm. Thermodynamics does pose problems for evolution, though evolutionary advocates fight it tooth and nail.
No, it most certainly does not have relevance to mechanism. One of the first things we teach freshman students about thermo. is that it tells you the end result and the direction of a process; it says nothing about the rate or the route.
The various statements of the Second Law all have an implicit understanding of the mechanism.
The second law is one statement (or two if you include the limiting case that the entropy change in a reversible process is zero). I have no idea where you get 'the various statements of the Second Law', other than your own imagination.
Thermodynamics does pose problems for evolution, though evolutionary advocates fight it tooth and nail.
Utter tripe.
No. Thermodynamic laws hold regardless of the mechanism; that's one of the points of thermodynamics. If a gas in a state (p1,v1) is brought reversibly to a state (p2,v2) in one experiment and brought irreversibly to the same state (p2,v2) in another experiment; the entropy of the gas is the same in both cases.