Bundle all of the wheels required for the package into a single package, rather than having a 1-1 mapping between OS packages and Python packages.
Then run it all in a Venv.
Then run it all in a Venv.
Also, you have to do that for python apps, for node apps, for go apps, for rust apps, etc.
As an user, I just want to run "apt install application" and have it work with dependencies kept up to date by the OS package manager and not have to micromanage the dependencies for all applications I use.