The package manager can handle removing pretty much any file it installs when uninstalling, so the host really doesn't get "polluted".
> or go back to VM overhead per application
In a development environment hosted on a VM, several applications can be installed on the VM (rather than having one per VM) to reduce overhead. Then testing and making code changes could be done by running a pip -e (editable) install and modifying code in the working directory, or making the change, repackaging and re-installing, and restarting the daemon.
With a container, at least in my experience, you need to re-build it each time you make a change to the code, which actually takes longer than modifying an editable install or re-building the wheel/RPM and reinstalling it.
In any case, the point I was trying to make is that the development cycle with containers, in my experience, is slower because you have to go through the build step every time you make a change. For an intpreted language like python, that shouldn't be necessary until close to the end where you test a fresh build before submitting the changes for review.
Couldn't the same thing be done via the package manager and a RPM spec or deb file where all the necessary dependencies are listed and installed as part of the package? It could be done on a VM or could be done on a machine by keeping track of what dependencies are installed when installing the application and handling uninstallation by removing all newly installed dependencies along with the application.