Use case:
User goes to skype.com, viber.com dowloads their debs, install them, some time later willing to clean up stuff and not a user of skype/viber/chrome/whatever opens the software center and looks for installed apps, it will not be in the applications section.

These debs are not in any local repo and even it they where the provider might change the package name at anytime, we can´t make these companies to provide as.xml data.

My idea would be calling packagekit with getPackages(Application|Installed), and if their packages is not in the index yet index the .desktop files