The effect on the prop I would see is that, in a low wing position, the prop's exit spiral is, by necessity, "split" into above wing or below wing airflows. Increasing the angle of attack by turning, while curving the incoming air upward to the fuselage, might cause that "split" to change in its above-below wing distribution, some of the "below wing" air "shifting" to above the wing. If that proportion of change is significant, this air would then be forced into a kind of "dogleg" path, which would lenghten its path, and so accelerate this portion of the air, depressurizing the corresponding area of thrust within the prop disc (in this case the below wing area).
The flow behind the propeller is anything but orderly. Many years ago I had to do some work with the stability of a twin turboprop. The simplistic view of the propeller slipstream may envisage a cylinder of high speed air trailing back from the prop disk. From the research that I did at the time, it appears that the air is split above and below the wing, which each half of the flow forming its own smaller "cylinder", although now a bit squashed. Due to a bit of sideflow, the two cylinders don't meet again in the same vertical plane - the lower one is usually displaced towards the wingtip, so the cross-section now looks like a figure 8 with a diagonal slant. The prop rotation can push them a bit as well, so if both your props are turning in the same direction, the left and right cross sections are not symmetric about the centreline. Add to that the fact that the"cylinders" are being subject to fluid shear at the boundary with the relative wind, and you can imagine that, even before reaching the tail, the shapes have started to break up. Now add to the the effect of nacelles, fuselage interference, etc....
So yes, I'm sure that the wing position and fuselage shape do affect the nature of the airflow. However, the stability impact of wing height alone is probably one of the smaller variables. It may be instructive to look at the Cessna Caravan and then some of the military trainers, all with similar engines. Are their varied handling characteristics solely a function of their wing height, or do planform and inertia play a bigger role?
By the way, why don't you have a look through the old NACA data and see what they have on the Grumman Wildcat stability.