Would you really be certain a commercial company buisness is going to care about correctly packaging for a flavor of linux?
Some companies wil do this, even more so if they work with FOSS and linux.
But in general, especially for companies on the proprietary train, I wouldn't be so sure.
If skype is in the base set of packages, I'd expect debian to require proper packaging. But if this is in some third party package, there are no such guarantees.
That said, maybe some third party package that just installs the normal (auto-updating) version into /opt or /usr/local might be an option. It is better than having no installer, and shouldn't break too much of your package manager.
Proper clean-up on uninstall is the only real issue I can think of.