What part of the OS should managed the packages?
The OS package manager. This is already a thing with Python in apt and pacman, where it will give you a fat warning if you try to install a package through pip instead of the actual OS package manager (i.e. pacman -Syu python-numpy instead of pip install numpy)
For this to work with a desktop PC, you would need to connect your display cable to your iGPU instead of your dGPU. The driver should take care of the rest. This might yield lower performance when using dGPU for processing (probably unnoticeable, depending on circumstances).
Windows 11 is objectively the better system, it just has too much garbage as well.
https://github.com/schollz/croc