It has been a long standing thing that stab position does effect KE flight, however recently designers are moving away from this and focusing on rudder areas above and below the thrustline as it apparently proves to be more effective in reducing pitching in KE.

Ollie

I dont think you are missing anything, I agree with what you are saying, but it has been my experience with most of my pattern planes, that they pitch to the belly in KE flight when setup to fly a perfectly vertical downline. It is usually minor and I just mix it out.