Supination is typically a structural issue which means the gamet of corrective magic that we often read about may not be as useful to you. We can not change bone at an appreciable level. Wolf’s Law always applies, but to suggest that specific repetitive loading will change the bony shape of the adult foot is probably not very consistent.
Before giving up on the structural foot, I would first recommend seeing an excellent manual therapist to see if indeed there is so more functional play in the foot. Soft tissue work, joint mobilization or manipulation can all be part of bringing your foot a little farther out of loading midstance in supination.
If this clinician has a lot of experience in working with feet and ankles, they might also be able to recommend an orthotic that will work for you. I know you said you’ve tried before, but there may be some other things out there to try as well. After some manual therapy, if there is some guidance for the new shape of the foot during loading, this is something you may need for the whole program to stick. I am very much in favor of orthotics in terms of the folks like you that may actually need them all the time to compensate for a structurally abnormal foot, but also in terms of using the orthotic that can be scaled away little by little if you don’t need it anymore.
While you are addressing the foot, you can still work everything about the knee as you would normally. By using the kneeling and/or half-kneeling positions, you will spare yourself of the bottom-up reactions that your foot and ankle are feeding the knee, etc.
It’s hard to be more specific than that, but I think you can try to get yourself in the hands of an excellent manual therapist, even better if they work with feet a lot. Orthotics and continuing to correct and/or modify your training in the short-term should give you a better picture. With a bony abnormality, orthotics are going to probably be part of the answer.
Sorry I can not do better for you without seeing you, but if you are not in pain, hammer away at the FMS weak link in conjunction with a more passive approach to reset and/or reinforce the foot. Reload it when the time is right.