[3.13] gh-129296: Fix `pyatomic.h` include paths (GH-129320) (#130667)

gh-129296: Fix `pyatomic.h` include paths (GH-129320)

Use relative includes in Include/cpython/pyatomic.h for
pyatomic_gcc.h, pyatomic_std.h and pyatomic_msc.h.

Do a similar change in Include/cpython/pythread.h for
pthread_stubs.h include.
(cherry picked from commit 3a974e39d54902699f360bc4db2fd351a6baf3ef)

Co-authored-by: Zanie Blue <contact@zanie.dev>