I don't know of an intention to break use of other makes but I don't know of any specific effort to test with various makes.  As you may have noticed, there were some significant changes to the Makefile rules for pgen-related targets by changeset 52597f888e7a which was released with 3.3.0.  I would start by looking there.  If someone can identify a problem, patches are welcome.

The thing is pgen shouldn't need to be run at all when using a release tarball (assuming you are doing that) as long as the preserved timestamps are correct (see http://bugs.python.org/issue14321#msg155910).  Perhaps there is a step missing in the creation of the release tarballs.  Georg?