Currently the pet bar location/position is tied to both Action Bar 2 AND 3. So if you have bar 3 active, but not bar 2, the pet bar will still be elevated, resulting in an ugly (and wasteful) gap of space between the pet bar and bar 1.
We can’t move UI elements around in Classic like you can in Retail (at least not without the use of addons, which shouldn’t be necessary), so please fix this basic UI component.