Making it clear in the code itself that something is platform specific is useful as well. Also, I'd say such stubs and extra files would clutter the project.

They can be made to work by introducing stubs for every os/arch/compiler/dependency I support, but that's way more work for dubious gain.

And who is to say I'm doing it wrong? Just because conditional compilation CAN lead to a rat nest doesn't mean it MUST. And if it happens to be well-organized and works as is, there is no problem.