Min RK added the comment:

`--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.

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Python tracker <rep...@bugs.python.org>
<http://bugs.python.org/issue22269>
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