There’s already some good advice here, especially about virtual environments which might be the most important new concept to learn IMO. But just to let you know - it’s not just you. The most generous view of the Python package situation is that there are a lot of different ways to do it.
I mean, I don’t know how comfortable I’d be bringing one to work, but the behavior you’re looking for (complex macros with swappable config files) remind me of pentesting devices like the Rubber Ducky.