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I would still prefer ~/.local/something-parallel-to-where-it's-usually-installed for its ease of documentation. But ~/.python/X.Y isn't terribly objectionable.
A minor point about Michael Foord's fallback proposal: I don't know why everyone is so keen to stuff things into ~/Library on the mac, but dotfiles don't go in ~/Library/Preferences. While that directory isn't exclusively populated with plist files, it's pretty close. If you want to try for consistency with platform convention, 'org.python.distutils.cfg' would be a better name for it, but I've never hand-edited a text file in that directory either and I get the impression one isn't meant to.
But, since framework builds of Python already has ~/Library/Python/X.Y directories that they look in for other things, that location should probably be recycled if one wishes to have a fallback.