1. Shorter crank arms will drop the foot at 12 o'clock so the rider will have less knee flexion by just installing shorter crank arms, but, the byproduct of this will be an increased knee flexion at 6 o'clock.
2. To accommodate the same 6 o'clock knee angle, you will need to raise the saddle height to get the rider back to the same 6 o'clock knee angle position as before, which will open the knee angle at the 12 o'clock position even more.
So not sure how you are calculating the knee flexion (12 o'clock position) will be the same?
I meant your knee flexion will be less on the upstroke even if you don't raise your saddle. True that knee flexion will be more at the bottom of the stroke, but is that really a problem? It's on the upstroke that is the issue.