Mercury has transom-engine height dimensions in their Optimax service manual. Basically says that bottom of transom to top rear corner of engine transom bracket to be 20 inches (for a 20" transom mounting midsection) for speeds under about 50. Over 50 it shows comparative data for speed increases with engine jacking above 20". it also shows impact of temperature and altitude on speed for a given rig-setup-load.
Tricky as stated by Mr. Hicks on dead rise transoms. I just bought a well used boat with 12* dead rise at the stern and it came with the engine bolted in the 4th hole down which put it about 2" high on the transom (22").
This boat is capable of about 35-40....on a cold day going with the wind and waves, and going to tell you that having it jacked up is not the right answer. As soon as my lifting eye comes in I am going to drop it down at least 1 hole and maybe 2 (¾-1 ½")and that's guessing as Mr. Hicks said since I have a fair to middlin dead rise at the stern.
I want the Anti-ventilation plate (I used to call it cavitation plate too but was corrected on here...cavitation are the little bubbles forming on the tips of the blades and such) slightly below the hull because I need some bow lift and can't get it with the engine high......the AV plate can't get under the headwater, while trimmed out, to get the lift I want.......prop is a Ballistic SS XL, made for shallow running and bow lift and doing all it can.
For the record, usually I raise the engine (from the standard 20" position) and get better performance and speed, but the rigs were different and responded well to the jacking. As others have said, each rig and it's usage is a unique mechanism for one reason or another.