It looks like the Programs/python.exp change was done accidentally in revision 88a532a31eb3 (Issue 18093), so we should be safe reverting the relevant lines back to Modules/python.exp.

The configure script currently sets

LIBPL='$(prefix)'"/lib/python${VERSION}/config-${LDVERSION}"
AC_SUBST(LIBPL)

However there is a contradictory comment in the makefile:

# This goes into $(exec_prefix)
LIBPL=  @LIBPL@

It looks like the comment came first. $(LIBPL) was changed from $(LIBDIR) [presumably using $(exec_prefix)] to use $(prefix) in r86731 (Issue 9807).

This isn’t my area of expertise, but my understanding is $(exec_prefix) is for architecture-specific files only. If python.exp is not architecture-specific, perhaps it should go in $(prefix), and the configure script (and makefile comment) needs fixing.