Regarding your specific case of testing relationships between complexity classes, I don't see a lot of hope. It brings to mind, e.g., (Petr Hájek 1979), wherein it was shown that a number of natural complexity-theoretic questions you could ask are actually strictly harder than the halting problem.
A very specific problem I see is, to state comparisons between reasonably richly-defined complexity classes in your formulation, you're probably going to permit (to improvise some notation) the class $\mathbf{Karp}(V)$, of problems Karp-reducible to $L(V)$ for arbitrary NP-verifier $V$, to be defined, which allows the statement $\mathbf{NP} \subseteq \mathbf{Karp}(V)$ to be posed as an instance of your provability problem.
But the decision problem for statements of this form is computationally equivalent to the language
$$\text{NPC} = \{V \mid \text{$V$ is a poly-time verifier and SAT $\le_P$ $L(V)$} \}$$
and, assuming $\mathbf{P} \ne \mathbf{NP}$, NPC is actually $\mathbf{\Sigma_2}$-complete, i.e. one level up $\mathbf{AH}$ from the halting problem.*
Since you're concerned about automatically discovering independence of the statements in particular, it should be noted that as soon as a logical theory is known to be undecidable, it's always the independent statements that cause the trouble. If you restrict your attention to the statements which are provably true or false in your proof system, you can solve your problem just by enumerating proofs. Since the decision problem you care about is probably going to be undecidable (as per the remarks above), independent statements are guaranteed to exist if your proof system has a bare minimum of desirable properties (i.e. computably verifiable proofs).
Of course, none of this precludes the possibility that specific conjectures of interest about complexity class inclusions or separations will one day be directly shown to be independent. I think other responders are able to canvass the current state of the art on that possibility better than I.
*If you're interested in showing that NPC is actually $\mathbf{\Sigma_2}$-complete, you can reduce from FIN defined in Hájek's paper, first to a promise variant of FIN where only the first k inputs of the input machine can be halting if any are, and as far as I can tell you'll need to construct $V$ using a delayed diagonal argument a la Ladner's theorem. If anyone knows of a more succinct approach I'd be very curious.