I have one leg that is a bit off from normal, so my pedaling motion is intentionally not straight (figured this out with the help of a PT). Bones are straight, knee is not quite in line with them. I could compensate on platforms without cages or clips, SPDs make this difficult (have to loosen them up enough to create enough float). Speedplay Light Action fix everything for me, letting me point my knee out slightly and adjust my foot to compensate.

I knew the PT my family doctor sent me to was going to be interesting after the therapist asked me to walk across the room so he could see how my knees worked said "Can you do that again? That was... weird." It is working well. Even before the muscle building we did in my hip to help hold the leg outwards a bit started working I was able to increase my weekly distances 30% with less pain almost immediately. 18 months later my distances are up 150%+ per week, now with no pain from riding.

If you have trouble getting your motion *straight* most clipless can help with that. Really depends on what is causing your knee pain. If you're an outlier, like me, where you're causing inflammation by doing things the right way consult a professional.