Most of the work in this space is not focused on neural compilation (having a ML model perform the transformation/entire compilation), but on replacing heuristics or phase ordering, where the issue of correctness falls back onto the compiler. For pretty much exactly the reasons you mentioned, neural compilation isn't really tractable.

This specific paper focuses on phase ordering, which should guarantee correctness, assuming the underlying transformations are correct. They do train the model to perform compilation, but as an auxiliary task.