IMO, knee strain is caused by poor cleat positioning and not spinning fast enough.
sitting further back on the saddle puts less weight on your arms.
sliding your cleats behind the ball of the foot will prevent hot spots on longer distances.

the Q-factor and proper toe-in/out, as well as properly training your leg muscle sets will prevent strain. you should aim for a balanced leg muscle set. if one set is stronger than the other, it causes your leg to twist, which leads to injury.
if your bones make your regular stance toe-in or out, the cleat should be rotated accordingly.