From what you are showing us, the answer to How does scons handle non-existence dependencies? is that it does not handle them at all. Go and look at M. Moskopp

From what you are showing us, the answer to How does scons handle non-existence dependencies? is that it does not handle them at all. Go and look at M. Moskopp's graph. It has a lot of dependencies for non-existent files that the compiler would have used in preference to the ones that it actually used, had they existed.