I think the problem with standing techniques is, as you say, the torque on the knee when a turn in done incorrectly , ie, planting the foot and turning the hips. This is the mechanism of football injuries, when a players cleats dig in as he cuts and twists his knee injuring the ligaments and menicus.
I think the complaints from seiza and suwari waza, other than aggravating old injuries, may come a great deal from chondromalacia/patella-femoral syndrome, from forcing the femur against a too soft underside of the patella. And that this was before unknown to the person because they didn't do much of the 'usual' things that brings this to a patient's attention: things that jam the femur to patella that way, ie basketball, running, climbing stairs. Unfortuanately, while most pain in Aikido is from doing something incorrectly, and so should be able to be identified and corrected so so real damage is done, I don't see much a person with PFS could do other than avoid that which causes pain (and take NSAIDS).
As an interesting side note, I discovered when doing a high volume of prescribing doxycycline and Cipro a few months ago that one side effect of Cipro I hadn't known about was increased risk of tendon rupture...something to think about any time a physician prescribes ANY medication, even for non-joint related issues, is to ask about side effects. Another gentleman in my dojo kept thinking his back ache was due to age and rolling, until he mentioned it to his physician and found he was having rhabdomyolysis (muscle destruction) from his cholesterol lowering medication.