You have different amounts of forefoot varus on each side (the degree to which the front of your foot is rotated relative to your heel). The previous commenter is correct, weight bearing position of your foot/ankle is more important than a non weight bearing assessment. If you are over pronating to compensate for your foot mechanics then it will rotate your tibia and femur to compensate and thus can throw off your patella (most probably where your pain is).
I have very high arches and require shims under my cleats in order to correct for forefoot varus. You also seem to need different amounts of shims side to side because your varus is assymetric (which is fine, humans are not symmetrical).
You could try putting in shoe orthotics in your cycling shoes to correct for some of this and then clear wedges. A tip is to stand barefoot and compare your kneecap position when standing barefoot on the orthotics. You could even put a bit of material acting like a shim would on the inside of foot and compare again. Grain of salt because this isn’t on the bike but would give you a better idea of how your feet anatomy is affecting your knee anatomy.
I had a bike fit 12 years ago that put orthotics in my road shoes and 4 varus wedges under my cleats on each side. Life changing. I used to be unable to ride 20 miles without pain. Now I am very sensitive to clear position but when it’s right I’m pain free.
Good luck (also I’m a sports/ortho PT but NOT a bike fitter)