Ooops you are right, I messed up too in my explanation, I mischecked the code. root and home are mutually exclusive, not root and prefix. 

In any case, all those options are making it really hard to understand. 

I'd like to make this story easier in distutils2, So I'll move this issue in there.

Maybe we could have a --show-installation-paths option in install that displays the installation paths the install command will use, and from where the options were read from (and in particular from which .cfg files)