I believe that the factors you suggest probably are genuine factors, however, in the context of all of the other factors and variabilities would not show themselves as clearly as you suggest. When I consider the differences in handling between two otherwise identical airplanes I have observed, I don't attribute any one factor, I consider them all.
Yes, it would be unwise to extrapolate a 210HP engine to a multi thousand HP engine installation, entirely different planes. The certified general aviation airplane world does not have many 1000+ HP single engined planes.
the N1K1, had a mysterious tendency to go in "auto-rotation" during turning combat (flipping on a vertical or vertical axis, sometimes alternating both unpredictably)
Okay, but that sounds like a standard spin entry from too tight a turn, 'happens all the time with careless aggressive maneuvering of light planes. I would be surprised to learn that the manufacturer chose to reposition the wing on the fuselage because pilots were spinning the airplanes in combat. But, being an uncommon WW2 type, for which data is probably not held in the western world, I think in depth investigation can be a mind exercise, but otherwise has less relevance for modern airplanes.
Wing height on a prop-bearing fuselage seems to be a truly major handling issue...
I don't share that opinion. Hundreds of each type in civil use have found great success with suitable (and certifiable) handling - they just do not have 1000+ HP.