OK, now I'm getting really confused.
The way I see it, Looking at the pump as an assembly with a downward angled shaft, it wouldn't make any difference where you set the pump (forward or back). the thrust point will always be at the same height (compared to the keel). Unless you make the nozzle end of the pump itself longer or set the intake lower in the hull or at a different angle, or used a droop of course.
In my humble and sometimes ignorant opinion
. The reason to set the pump back would be increase the leverage the nozzle/thrust point has on the hull and to be able to make the ride plate long enough to be an affective adjustable hull extension .
I think I see where your confusion starts, if you set the pump back, the intake hole goes back with the pump, so the more boat you can get out of the water without ventilating...its hard to explain but the pump angle stays the same, the actual height stays the same but the "leverage" we're talking about comes from the change in distance from the transom. I drew a picture but somehow does not reflect what I'm getting at.
The blue lines are the hull.
The red line is the shaft centerline.
The green line is turbulent water (wash).
The violet is the intake area.
The thin black line indicates wetted hull area.

You can see from the shitty drawing that there is a lot of wetted area in front of the intake on the setback pump.
You can also see the entry area of the pump to the water is technically lower in the water do to boat attitude (they only sit "flat" on the trailer).
I hope this helps and does'nt confuse further. I'm sure Josh (JBP) can explain it more than me, we played with pump setbacks a lot on the aluminum boat (which with a plasma torch and a TIG welder can be done in about 4 hours) The difference is unbelievable.