Exactly right. There is an irreversible entropy to this: once a certain number of implementations exist, it becomes almost impossible to create a "new standard" that fixes them all, because it has to be backwards compatible with too many of them.

As someone responsible for probably one of your astronomer friend's tools (Anaconda), I have to say that we can only do so much: the nature of Python itself is that we cannot ignore what the user puts into PYTHONPATH, PATH, etc. On Windows, at least, we do create shortcuts in the Start Menu to ensure that we get a well-defined command shell. But if the user forces things like PYTHONPATH, there's not much we can do to un-fsck the setup.

Maybe it would be useful to have a python-safemode (or python-portable) binary that explicitly ignores all environment variables, configuration files, registry settings, dotfiles, etc. etc. and only looks at files that are next to it in the path....