This question is, and has always been, on topic.
The OP's reading of the FAQ is correct. A question about using built-in Ubuntu software and third party Ubuntu software on Ubuntu is a question about Ubuntu, and is on topic.
We don't consider questions about running Ubuntu software in Ubuntu to be off-topic just because they might benefit someone running Windows or some other OS, and it's dangerous to send the message that we do. Imagine if a Windows forum rejected a question about Windows because it might somehow also help Ubuntu users!
To anyone who disagrees: Look through the open questions on our site, and ask yourself how many of them might be helpful to someone running a non-Ubuntu OS. You'll find that many of them could be. Probably most.
Do you really want to close almost every question about bash or grep; repairing GRUB; using LibreOffice, Banshee, Rhythmbox, Firefox, Chromium, Chrome, or Midori; Nautilus, Dolphin, Konqueror, Thunar, or PCManFM; installing software from source code; or adjusting any system settings except the tiny number that differ from those in other GNOME 3 based distros?
I see no reason to keep this closed--I think closing it as off-topic was a simple mistake arising from its previous wording being difficult to understand, exacerbated by attempts to justify a mistake that never made sense in the first place.
We should reopen this now. But if for some reason people want to keep it closed, the OP deserves a reasonable explanation for why it ought to stay closed. More importantly, the community deserves an explanation.