> A) Is there any performance penalty on the compiled result due to being optimized in separate pieces

AFAIK, the answer to this is no but only if LTO is doing a good job and actually optimizing well across object files.

> B) If not, why isn't the optimizer smart enough to split them up internally and optimize in parallel?

I think there was another comment by someone more knowledgable in Zig that this is something which is being discussed by the Zig compiler team.