In some Linux distributions it blocks you from installing system packages via pip, often there are then packages which can be installed via your distros package manager.
With arch for example:
sudo pacman -S python-'package'
Or, as others mentioned using venv.
Probably a bit more polished UX (especially for not too tech-savy people)
but I’d say the biggest difference is integrated multidevice support, either via their cloud or selfhosted…