Ok so this is a reward from pursuing all the possible timestreams when you're working on saving willowbrook. One of them ends up with you fleeing the village and the cave and having a spat with the tea master rather than defending the village or helping the villagers. The bonded beast is a reward/path companion that stems from that.
I'm not sure if this is a mandatory flag because you can do everything in the game without it, it just has some small modifiers that help with a plethora of things.
EDIT: I think you should be able to get it without having softlocked your save just go back to willowbrook's start point and ignore the beast tide or something. Maybe someone with better memory or doorwatchers can chime in with the exact steps to get the pet.