My experience is: Mobs start attacking the pet, then I anchor the skiff, mobs starts attacing the skiff becouse my pet gets stowed, so I need to kill them (jump off the skiff), after I kill the mobs i can get back on the skiff (via F key).
Nevertheless, not stowed pet while we are on skiff is kind of bug. Same as it pet is not stowed when i got mounted raptor on the skiff 🙂