I'm not sure if PHP stores any compiled binary or byte-code at all. Maybe it compiles it all on each request. It's super fast though, even with tons of imports.
My guess would be that it keeps compiled versions of each file in memory and on each request, it walks down the whole import path. And when it encounters a changed import, it compiles only that one.
Would be cool if someone with more knowledge could shed a light on what is actually happening.