If I understand correctly, the normal way for the user to add flags is via compiler.cpp.extra_flags etc. But build.extra_flags overrides this so it doesn't do anything. And overriding build.extra_flags is not an option either because this would delete the values that MiniCore is using.
Edit: Sorry, I'm confused, they do seem to be separate things. But boards.txt does also set compiler.cpp.extra_flags in some cases.