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`--prefix` vs `--user` is the only conflict I have encountered, but based on the way it works, it could just as easily happen with any of the various other conflicting options in install (install_base, exec_prefix, etc.), though that might not be very common.
There is a general question: If a Python distributor wants sys.prefix and default install_prefix to differ, what's the right way to do it? Setting it in distutils.cfg makes sense other than the conflicting option issues. Could there be a special `default_prefix` key that gets used as the final fallback (end of install.finalize_unix)?
I would really like to avoid having a warning on every install, since warning suggests that something has been done incorrectly, which in turn suggests that `distutils.cfg` is the wrong place to set the install prefix.