Dug a bit further here.

The issue is that CFLAGS_NODIST will always come after normal CFLAGS (which are subsets of PY_CFLAGS and PY_CFLAGS_NODIST) [0][1].

The EXTRA_CFLAGS variable is appended at the end of PY_CFLAGS [2], hence as reported here, whatever compiler flag comes after, embedded within PY_CFLAGS_NODIST, will override the previous flags if they contradict each other.

So basically EXTRA_CFLAGS can be used only for flags that can't be overwritten by PY_CFLAGS_NODIST, which in my opinion, is not very useful in the context of just adding extra flags.

Commit adding the variable to Python 2.5: https://github.com/python/cpython/commit/08cd598c2145d00f1517c93cabf80a5d7d2a4bc0

"EXTRA_CFLAGS has been introduced as an environment variable to hold compiler flags that change binary compatibility"

Apparently it was added in order to avoid using the OPT variable for the various debug builds described in https://github.com/python/cpython/blob/master/Misc/SpecialBuilds.txt

On another note this flag will get passed down to distutils, so if it was used for building the interpreter, C extensions compiled by users will also inherit it.

Honestly I am not sure what the best solution would be here. If the various sub-debug special builds are still relevant and they stack, by doing for example $ make CFLAGS_NODIST="-DPy_TRACE_REFS" EXTRA_CFLAGS="-DPy_REF_DEBUG" then the issue can be closed, and the documentation can be more explicit that the EXTRA_CFLAGS is to be used only for the special builds.

If the EXTRA_CFLAGS can also be used for adding our own flags, then the flag handling needs to change to take this into account.

[0] https://github.com/python/cpython/blob/master/setup.py#L85
[1] https://github.com/python/cpython/blob/master/Makefile.pre.in#L115
[2] https://github.com/python/cpython/blob/master/Makefile.pre.in#L97