I'm sure this thread was a great help to the OP...
Can someone please explain to me from an anatomical, kinesthetic, and physiological point of view how seiza/shikko/suwariwaza damages the internal structure of one's knees. Because I don't think that it does. Abrasion and bruising to the skin definitely, but doesn't give someone bad knees.
Regarding stretching and warm ups:
If we kept ourselves healthy no warm up would be necessary on most occasions. Unfortunately, the vast majority of us are not healthy, and then proceed to add poorly performed physical activity in too large a quantity on top of it.
Very simple really. You ever twisted an ankle? In suwariwaza the knees are now your 'feet.' Put all your weight on a foot and twist around and you'll cause damage.
Then there is the fact of the knees are not built as a joint the same as feet and can be a tender point for some but basically it means they need to get used to it.
Done correctly I agree with you that it doesn't give bad knees and in fact will make them stronger but it is best to also be aware of the various factors that can lead to damage.
I also agree with the point you make about health and I have also said so myself, not that I expect many to know about too much to do with that especially when it comes to joints and nutrition but as you say health then it's best to know from that viewpoint what the problems for some are.
For instance....I have trained with weight lifters and carpet fitters. These two things are where lots of knee damage has usually already been done before they attempt any suwariwaza. Thus they can find it very uncomfortable. So it's not always just down to assuming all knees and conditions of knees are the same.
Technically the damage has been caused by too much stress being put on their knees in their 'work' or activity. What damage is done? Well ligament strains is the usual thing and over time this actually causes build up of calcium deposits in their knees which in turn interferes with knee operation. As you see this is thus internal over time.
I remember one weight lifter who started many years ago and he carried on and did very well for he is now the top student at my old dojo. However, he had problems doing anything from the knees even though he was like hercules unchained. Anyway with advice he went to get it all checked out and low and behold he found what we said to be true. He actually had an op with a local anesthetic in a hospital and I always remember his description. He said they pulled out a white disc from behind his kneecap....made of calcium deposits buildup.
It's ok for youngsters but but only apparent later in life when you find out you have been doing something incorrectl;y for years and now suffering the reality.
So acting from fear to me is not the answer for that leads only to voices shouting about how dangerous and damaging things are. No, acting from sense means be aware of the 'wrong ways', be aware of the correct ways and also be aware that things can actually be strengthened.