Thank you, that was a good idea. I opened up those settings and played Russian Roulette with the different options using the Magitek mount, and I ended up finding a setting combination that at least allows me to use Special Pet abilities in instances and duties (the Pet Hotbar loads when I mount, and responds to keybindings).

I still can't figure out any way to keep the separate, redundant Pet Hotbar hidden now, the way it was before 3.3.

I also had to make a hotkey for "Change to Hotbar 1", because that's the only way I've figured out to fix my Faerie / Garuda abilities replacing my normal Hotbar 1 every time I dismount from a Special Pet.