This is unique on Windows. I actually took a look at dconf on my machine and no application occupied more than one key.

GEdit sits in /org/gnome/gedit and virt-manager in /org/virt-manager as you'd expect.

I also hate Android's behavior, since there are situations where you want to keep them. If I remove GEdit for whatever reason, I expect it to keep my settings.

There are legitimate reasons to criticize Gnome, but this isn't one of them. dconf is totally reasonable and has significant advantages over plain text.