> Because we don't want to maintain more config options?  Really, I don't to want to further complicate our build process.

I don't see how adding an option to make one path configurable would make the build process more complicated.

It seems like Xavier and Thomas do use Modules/Setup for their need, and for me it's strange to have to modify Modules/Setup (or Modules/Setup.dist) if it's tracked by Git. If I modify it, IMHO it's a configuration file, and it shouldn't be part of Python code base. It's fine to have a default configuration, but if you don't want to  use the default, just pass the path to your own config. No?