Since you're talking about how aikido applies in the real world and real situations, like an ambush or whatever, one of my biggest problems trying to practice aikido movements (tenkan/tentai) on real-world surfaces and wearing real-world footwear is that it absolutely KILLS my knees.
You know, I am currently teaching a class of Nat Guard soldiers for the next week that have not ever done combatives training, several of them were complaining about knees hurting from going up and down and rotating on the mat.
Not sure if it is related to what you are talking about...maybe you are talking about the torsional movement/pressure while standing in footwear??
I don't seem to have this issue at all....I will have to watch what they are doing.
I know in my dojo back in the states my former instructor spent a great deal of time teaching us to move and transfer weight correctly. Same on the Mat....my knees don't really "rub" or rotate on the mat.
Again, I may not understand it correctly what you are saying, but slow down things and look carefully at what you are doing. If you are used to "gliding" your barefeet across tatami...you may need to re-evaluate and adjust what you are doing.
same with ground fighting...knees and elbows are not transfer or weight distribution points for me a whole lot. I had to learn and develop strength and coordination to avoid this. Play with it and see!