When I use python extensions (often written in C), this problem doesn't arise because distutils, and sometimes cython, handle everything.
Python isn't the best C build system, but frankly it scores better than cmake and friends for ease of use.
All the installed tools and libraries are old as hell and rarely get updated, and it's riddled with quirks and tools that are subtly different on osx. I hear it's gotten better with Mountain Lion.
Thank god for homebrew.
Interesting what you say about 10.8 - I might give it a shot then. I will be upgrading soon from snow leopard (2009 MBP) and I was going to wipe and go debian/XFCE, because of all the "new ideas" like "let's not have save as" etc, but if installing stuff is easier (and I know multitouch works) I might give it a go.
But I got stuck with it because I had to do ios dev at some point, so I learned to adapt ...
I hear arch and ubuntu both work great out of the box on macbooks.