Packages tend to thrust some completely idiosyncratic configuration scheme down my throat that is documented nowhere and that creates conflicts of its own. They don't just solve dependencies they encourage dependencies because they are supposed to be resolved automatically anyway. But they're not. Things break all the time. The Linux dependency hell has far surpassed the infamous Windows DLL hell of the 90s.
I was called to help people fix their Ubuntu installation after some package upgrade had uninstalled half the system. I had an upgrade replace a working but proprietary wifi driver with a non functional "free" one, etc, etc.
Most of the problems I ever had with Ubuntu were caused by that completely broken package management idea. If I want Python 2 and 3 on the same system I can't have a package manager tell me that's not supposed to be when I know full well that it's no problem.