The purpose to sit engine at the sweet transom height reflects the need to make the most out of that portable engine, on larger engines not an issue, thus having more HP will compensate much better any tail water drag as opposed to less HP engine in which you need to take all those stated ponies out for top engine and boat performance.
Let's rig the Jon boat as if were your first boating day :
(1) Float boat alone and trim engine to be perpendicular to water level (90 deg) usually second, third hole out transom.
(2) If alone move fuel tank and any other heavy objects forward, if not, seat one passenger up front to have a well distributed deck weight.
(3) Go for a wot spin on flat calm no windy water condistions, being spot on trimmed, anticav plate and boat's hull should ride parallel to water level provided that deck has well distributed weight.
(4) Visually check by pulling your head out transom if with any back or over transom water splash. If engine produces a neat flat middle wake you're ok, if with over transom splashes, engine sits too low, water flow at speed is passing over small upper water deflector plate (yellow line) and hitting round middle leg portion. Will need to raise engine accodingly with wooden shims till water flow passes at speed slightly underneath small water deflector.
4 This is the sweet engine/transom height, once dialed there's no need to move trim angle from initial set position, engine will deliver its top thrust and water flow will be nicely cut at the sharp edge formed between small water deflector plate and lower anticav plate producing least tail drag while achieving top hole shot and close turns with no prop aereation.
Have no experince whatsoever with Jon boats but these principles can be applied to any boat as well, try them out. If you manage to sit engine at the sweet height, any prop pich you test will work top. Can go for the 7K max wot mark if you want.
It there's a point that you don't fully understand, let me know.
PD : The only way to determine at which lower tail height water flow is passing by when boat is on plane is pulling your head, this is not a assume, guess not even asking at the forums issue, must be checked while at trial.
Happy Boating