Couldn't the entire question of whether Size affects the starting Intelligence of all creatures be answered by looking at the creature generation rules in HoH: Mystery Cults, Bjornear? It is my recollection that they do apply. You get a benefit to a large Size, this benefit is off-set by being forced to spend Virtues on bringing your Intelligence up.
Its quite possible certainly. Except i dont have that book(although i can get access to it from another player), and anyone starting out with the game definitely isnt likely to have it either.
And for an magical animal companion, you dont have the option of spending virtues to bring intelligence up. At least not without getting additional rule books. AND something that says that the limitation in the flaw actually doesnt really count except when it does, but not quite... Or something... 
Apart from that, big size isnt automatically a benefit. Having a bear walking next to you "everywhere" is going to cause no end of problems, that is NOT a benefit.
Nor is the connection a good idea as you might understand when you hear of the proposition to abuse the rules by having a hyperintelligent magic flea, by one of our more "inventive" players... :mrgreen:
Gamebalance advocates, fear thy munchkin!
And really, whats the point of having a magical animal companion that is dumb as a rock? Its totally selfdefeating. And requiring a rule supplement/addon for something in the base rules to become complete, thats just bad, very very bad.
There are no rules in HoH: Mystery Cults relating intelligence or cunning to size (at least that I found in a cursory search), this was the source of my confusion up thread.
Another angle is simply consider the animal's inherent intelligence/cunning or its "mythical" equivalent. E.g., in lore owls are known for their great wisdom, so an owl companion would have a high score. Crows and ravens as well, but perhaps a bit less than the owl. Raccoons and weasels are very clever, and this was noted by even ancient observers. Horses are notoriously dim-witted. Bears are clever, too, but not on par with the owl or weasel. You get the idea.
And it's not out of the question for there to be a super-intelligent horse, just discuss it with the SG and your troupe.
Good idea. But why do I think of Jolly Jumper? 