Steam already does this on Windows. They make fake installations entries in Windows witch soul purposes is to evoke Steam when you hit uninstall. The same could be done wit apt. Applications installed via steam would show up in your favorite package manager tool but the actual installation would still be handled by steam. This could even be used as a good way to leach on to the dependency resolving of the system instead of how it is done on windows where every game reinstalled the same 3 libraries over and over again.

