Lysander wrote: So it's possible, indeed. I'm guessing that's what happened.
You wouldn't really have to guess.
I hesitate a bit to say much more because people often don't want my oldschool advice but you generally are a quick study and you've never growled at me.
If, especially while changing things and trying things out, you were to record in a log book, you could have checked if the timestamp on the file was the same as the date you installed XFCE, for confirmation. That would be easier than having to parse back through your dpkg.log's to find it, with a lot of activity, it's probably already gz. But keeping a log book isn't something most home users do, although it has some potential to help while you are still trying things out.
Since you've chosen GNOME and no other DEs, that file is useless and unnecessary until such time as you add another DE that would use it and overwrites it. And, in this instance, it interfered with the way you wanted to use your system.
@HoaS, do you know if the GUI, Synaptic's "complete" removal would have removed that user configuration file or not, I don't know. I'm still oldschool apt-get most of the time.