I have your same problem TS, if you find the solution or useful informations, please PM me.
When i was a teenager i went to the orthopedist and he told me, if i remember correctly, that my patellas are at a particular angle that make me consume my cartilage.
He thought about some hyaluronic acid infiltrations, but i stopped completely squatting and activities that make me load my knees and the pain stopped, but i still felt like my knees are not made to be overloaded.
Now the pain reappeared because i started doing trap bar deadlifts, no problems with normal deadlift, lunges or every activity that put pressure from the top on my knees with knees at 90 degrees, are the worse.
Yesterday had pain in my right knee from biking, during a climb.
Also, my right knee pops every time i extend the leg, like something is moving from its place, and the left knee doesn't bother me very much.
These are all the info i can tell you, stopping the activity that causes pain is the only thing that helped me.