JR,
I suspect it's what was used as reference points, or an optical illusion. On my Broadbill, using a strait edge on the cavitation plate of the Yamaha 15 to measure to the bottom of the keelson shows 1.5". The Yamaha manual says it should be 0-1". Being my first boat, I just followed the plans as closely as possible, and it worked out ok (except for the transom angle issue where I later had to make a shim to add more in). The 9.8 Merc did 17-18 mph empty, and the Yamaha does 25.5 mph, any load. Have not tweaked the Yamaha any (such as changing props or engine height) to try to pick up more speed.
On the Brant II I acually played with the engine height. Using the same measuring technique (and I'm not sure what the right technique is, because the hull is curved, and the boats sit at different angles in the water at differenct speeds) the measurement is currently 0". I found, in general, that by shimming the engine up, the boat went faster. Any higher than where it is set now, and the prop "blows-out" on sharp turns, and the boat feels "loose" on the water. At 0, I have to slowdown a little on sharp turns, and can make the boat blow-out while turning donuts, but was trying to tune for max straight speed.
Have you started cutting wood yet?
Take care!
-Bill