You're not strictly correct there. To clarify for others reading Coding requires 250mm FREEBOARD at the transom.
If you build the deck up to the top of a transom that gives 250mm freeboard then you won't trap water in the boat.
Most of the larger Halmatic RIBs do it this way.
Duncan, a fair point and maybe I was being a bit too general.
Freeboard will be taken from WL to the top of the transom (at its lowest point). Of course if fitting outboards transom height will be dictated by shaft length/cavitaion plate etc. All of this will relate to how the vessel sits in the water ie. prismatic and block coeficients of the hull form. This in turn will dictate performance, fuel etc.... a long debate for another day !
If as you suggest you build the deck at the 250mm level then there can be issues with MCG/stability especialy when you have vessels with careful and fine lines. A Pacific has more displacement and less fine lines enabling a higher deck line.
If transom height is too low for coding then a second internal transom could be built( note some of the Deltas and Avons). This in many ways works well but still creates the captivation of water. Also noting your point that it is better to keep the engine as high as possible for obvious water related issues.
No such thing as a perfect boat !!