Uh, didn't Altair look exactly like Desmond? Ubisoft based both designs on one actor/model.
Like you said, we never see Altair without his hood, so basically only his face from the nose downward is viewable in most circumstances. Desmond's facial features from that point down is practically the same as Altair's, so HT could just base their sculpt fully on Desmond without having to worry about Altair's hair style or whatever.
But.. then we'd have a Desmond Miles figure, not one of Altair . I mean, Ezio also had a resemblance to Desmond (since he was Desmond's ancestor), but you could still tell their faces apart .