First, I would count Google in the extremely skilled category :-)
(cc'ing Thomas so that he can chime in)

Second, if someone are doing a custom build of Python, they are very likely modifying something else than Modules/Setup (*).  So they already have some kind of custom branch or fork of CPython tracking their own customizations.  Why Modules/Setup can't be handled the same way I'm not sure I understand.

(*) see for example the Anaconda build of Python, which modifies several files but *not* Modules/Setup: https://github.com/AnacondaRecipes/python-feedstock/