It's more than an implementation detail. With an intermediate step of source code compiling & linking, there is a mechanical process checking for well-formedness that would otherwise be skipped. This is especially important if you're editing a large codebase, which even your agent's private-only repo would benefit from.

There are also times when you want the final product to be able to target different architectures and platforms. Generating into a higher level language allows for re-targeting the code by only changing a few compiler & linker flags or runtime/environment config. I would much rather that than hoping the LLM is feature- (and bug-)compatible between generation runs.