Hello Daniel,
regarding stabs height, I don't know. We have to wait some expert to come here...

For the up thrust question, I'm quite sure it depends both on thrust line placement and fuselage shape: in fact, planes are not symmetric with respect to fuselage frontal area. If we have more surface under the thrust line, a torque will originate since the lower portion of the airplane is generating more drag than the upper. So the up thrust is used to overcome this issue. I don't own a fixed gear pattern plane, still have a retract one, but with the fixed gears wheels and pants are all generating drag with a good arm with respect to thrust line, and I bet that with those planes less down thrust is required, or up thrust actually.

I don't know if there are other effects, however.