[Answer]-Whether to (and how to) handle multiple many-to-many relationship through a common intermediary/join table in django?

I would suggest to keep your initial implementation as simple as possible (e.g. no proxy table no overwriting save) and not to worry about number of tables unless you reach some pretty amazing numbers, hit some kind of serious issues with it or or outgrow the usefulness of “simple tags”. This might save you one hairy implementation that you might have not needed in the first place.

P.S. I am using https://github.com/alex/django-taggit which is pretty handy and easy to work with. Just saw that the repo has ~60 issues in gitgub 🙂 but I have not hit any of them.