MHWIB - It's still a monster
The Commander is a liar. It's still a monster, so its head must be a weak point he said. But that's not true for all monsters, not even Fatalis if you use ranged weapons (his head is not weak to shot dmg even after tenderizing).
It's just a joke meant to pick on his choice of words.
But generally, the head of a monster is a weak point, especially for melee.
so please equip that flinch free and hit the head together.