It appears to be a minefield subject and here is my can of gasoline to throw fire on the confusion of your resolution.
I have, until recently, used SPD-SL extensively including on long distance/ultra rides. I am lucky enough to have found comfortable shoes and there is enough options with cleat movement to work through pretty much all of knee pain issues to date. My personal situation is that I came to cycling as a middle aged ex rugby player/ distance runner who is tending towards clydesdale and had consequently put a fair amount of mileage on cartilage etc. (Several clean ups but no major surgeries)
I managed to ride comfortably (in the cleat/knee department at least) through one and a half TCR's (comfortable being a relative term in those situations of course) In fact, on previous shorter tests I had binned thoughts of using MTB type cleats ultras due to discomfort from both shoe and cleat after many hours in the saddle and found the road cleats better.
I did get knee pain when racing though, but have concluded that it is from pushing a big gear/mashing with a lot of force. (I use a 53/11 when racing)
I recently experimented with flat pedals for non racing rides, and quite frankly its been a revelation. I had initially tried them after having issues with mounting/dismounting when fatigued on a loaded bike in hilly terrain. I had assumed that they would feel "floppy" and my feet would be uncomfortable after longer day rides. But thus far its been amazing. Sure the power transfer is diminished, but comfort wise, and hopping off the bike is s easy. I just don't seem to notice knee/tendon issues at all. Aces.
I haven't put any back to back super long rides in, which could of course throw up issues, and I do appreciate that it is a very subjective topic. Different strokes for different folks etc.
I hope you get to the bottom of your issues, you are riding TCR this year right?