Tarek also answered my questions.

1) 4) build and install options should be defined and checked only once, in configure. build and install would inherit from this class and get their option from it.

3) I switched to using distutils2.core.run_setup, which Tarek said is okayish. Understanding why the usual idiom of using the classes directly doesn’t work will be better.

5) Since the cache file (the file that contains options, written by configure) is tied to a precise build, it should be specific. I can put the platform and Python version in the filename, or maybe put the file in the platform-specific build directory. Not sure about the naming in dists. I still have to think about the overlap between setup.cfg and configure.cache.