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Stéphane, as I understand it, this issue covers two problems:
(1) Building and installing shared modules using Modules/Setup was broken for current Python 3 releases;
(2) Using those shared modules when running Python from a build directory (rather than from a normal installed Python) is broken.
Problem (1) is now fixed. Problem (2) remains to be properly fixed; it's a little tedious to get right as a fix needs to take into account the SO_ABI and ensure built modules get properly cleaned and all the right Makefile dependencies work. I'd be happy to review a patch if someone gets to it before I do. But it seems to me that (1) was the serious problem; (2) is more of a minor annoyance for developers with easy workarounds, e.g. use PYTHONPATH or install Python to a temporary location for testing.