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Even if you check for -fmax-type-align compiler support at configure time, there is a potential problem:
Nothing guarantees that extension modules are built by the same compiler that CPython is. If CPython used an old clang without support for that flag and the extension module compiled by that CPython via pip and setup.py, etc. uses a more recent version of clang - it wouldn't specify that flag and the extension module code could be broken.
I suppose this issue of conditional compiler flags is nothing new. It should not block us from going forward with a workaround like your PRs for now.