The rules could be better here, yeah. The bonus you choose should follow from the fiction in some way.
The animal companion follows your command to the best of its ability. The bonus mechanically reinforces that, the rest is up to the GM.
You say "I tell my dog to fly!" and the GM says "I just looks at you and cocks an ear."
You say "I tell my dog to tackle the orc shaman!" you make the roll, choose your trained for combat bonus, and the GM says "It grabs the shamans arm and drags on it. It's not enough to actually bring him down, but it does open him up to your attacks."