Those all seem like pretty basic developer best practices to me.

Of course each project needs it's own virtualenv. In fact, each project should have it's own docker image. Why install an application library to the entire system? That is not a good idea in ANY language.

And of course scripts need to use the right virtualenv. Or better yet - why not put each app in it's own docker? That bundles up everything into a single "file" you can run on command.

All of these things you are listing as downsides seem like things that one normally moves away from, when they put a codebase in git and stop deploying to prod by copying a few files to a shared network drive and restarting the server?????