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My short shaft jet outboard sits 2-1/2" above the transom to tuck properly into the jet tunnel.  I've just run most of my boats the way they were set up when I got them so I never paid close attention.  With this jet tunnel boat, the previous owner had a prop motor on it which I sold when I got the jet.  I had to make multiple adjustments to get the height for best performance and least amount of spray back.  I also had to add transom wedges to get rid of porpoising.  With a clamp on motor, I'm not sure I would want it mounted too high, but I've never had a clamp on so I might just be over cautious.