While, this does not fully answer my question, it seems like "guess-and-verify" translation makes this question less important. Because defining "verification problem" does not depend on computation formalism, thus clearly works for recursive functions.
It does cover one of the motivations for my question. On wikipedia page for "propositional proof system" there is a claim "One can view the second definition as a non-deterministic algorithm for solving membership in TAUT", which was unclear to me. Looks like it is just informal usage for such "non-determinism to verification" translation, so it does not require formal non-determinism definition.
Another (non-formal) complication I see is that non-determinism is (at least in formalizations which I have seen) related to small-step semantics, while recursive functions are essentially big-step.
AFAIU, they define set of computable functions, but "forget" computation steps of their execution, just like big-step semantics do. This should make defining of "number of non-deterministic choices" more complicated.
Thus verification formalism seems much better fit for recursion formalisms. Not only that, it seems like size of proof certificate essentially encodes number of non-deterministic choices taken.
It may be that papers on non-determinism in FP should be more relevant then internalizing choice operator into (general) recursion formalism.
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