Why using independent package managers alongside the system one? I think the introduction of non system packagers is what brought us the whole mess we are in. Most system packagers allows for custom repositories.

Because the system package repository doesn't package everything & isn't always up to date. And if you introduce other repos to fix this, then you have an ecosystem with multiple instances of the same package distributed at different versions in different repositories, and God help you if you need multiple versions of one package, or if you need a different version of Python entirely. Nix could do it, but not anything else.

No—system python is for the system's scripts, and user projects should have their dependencies sandboxed in a virtual environment. That's the only model that really works.