I transitioned from tennis shoes on rubber pedals to tennis shoes in toe clips on serrated road pedals to leather racing shoes with metal cleats on road pedals in toe clips to racing shoes with plastic cleats in toe clips to SPD pedals with little float to SPD with more float.
The fine tuning I saw necessary with clip less was pronation/supination adjustment. But the slight discomfort and adjustment came in the context of high horsepower output in race training not touring efforts. There were MANY other adjustments of much greater significance in race training than getting the foot position right since that was so fundamental.
The folks I knew who got knee problems did it to themselves by pushing past the warning signs, repeatedly.
Maybe the brothers could benefit from a different shoe pedal fit, or a lower hp effort.