But my main issue is still here (double click on a desktop folder triggers Dolphin instead of Nautilus *in a Gnome session*). Have you any ideas about anything that could cause this? It's very frustrating.
A while ago I had a similar issue. Firefox would open folders with dolphin instead of nautilus, even though I was running GNOME and I had set nautilus as the default for inode/directory.
It turned out to be a conflict between two DBUS service definition for the same interface (org.freedesktop.FileManager1), and as a workaround I created a symbolic link in ~/.local/share/dbus-1/services to nautilus' service definition (/usr/share/dbus-1/services/org.freedesktop.FileManager1.service).
As I understand it worked because services defined in ~/.local/share/ have a higher priority. See https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html...
I don't know if the desktop uses this DBUS interface specifically (or if it uses DBUS at all for this matter), but it may be worth a try.
BTW the thread about "xfce4-notifyd issues" also mentions conflicts between DBUS services.