Certainly a lot of these issues exist outside of Python. However, we can solve them in Python, whether or not they are solved elsewhere.
I can figure this out for myself, and I feel we're getting close to where we need to be at work. The problem though is that, having figured it out, the only way to express this is as a bunch of additions and configurations to the system, some practices, and some guards. I just want us to agree on a good way that people should do this -- it's not a technical issue. And the tools should not just support that practice, but encourage it, with one set of conventions.
Right now one of the reasons some people balk at setuptools is because it solves problems they have already been solving on their own with hacked setup.py files and sys.path hacks. Setuptools breaks a lot of these hacks (it tries really hard not to break too many, but it is inevitable), since it is actually trying to come up with an inclusive way to do these things. I think some people have become comfortable with their own practices, and have forgotten that other people don't use those practices, don't know what those practices are, and don't have any tools to help them go down that path. So, that's what I'm complaining about -- the default distutils configuration, and the default sys.path, and the default site.py, all encourage bad practice. They don't stop you from doing things the right way, but they don't help either.