My impression after 3 different engines on two boats, is that dealers tend to mount the engines low. On both boats, when the dust settled, I was running in the bottom hole (highest setting) and I wish I had another hole. The only problem was on both boats there wasn't enough transom left to raise the motor. On my 150 Yamaha, the original dealer set it up with the cavitation plate a good 2 inches below the bottom. I think most dealers are thinking V-hull with dead rise and not thinking flat bottom.
I like Bob's approach. I just ran this last weekend with a Permatrim installed, and I believe I am at the correct height if not about 1/2 inch low. I can see the Permatrim through the spray over the cavitation plate.