I entirely share your view about working with system packagers. The current distutils infrastructure is really hard to work with (and I have considerable experience with it, as the main maintainer of distutils extensions in numpy for the last 2-3 years).

From the start, bento packages can be installed so that they respect the FHS, exactly like autoconf packages. I also hope to make compilation more customizable (which is a real PITA in distutils ATM).