I'm not sure that anyone is actually advocating that the AV plate must be level with the bottom of the boat, but it's generally a reasonable starting place. This is Locozodiac's take on the subject for his perspective on things.
He sent it to me as a Word doc so I've just converted it to a pdf and uploaded it here.
That's funny, if you check here and the other side of the pond boating forums, posters inquiring advice on motor/transom installations will receive such answer which I read all the time..