For your popliteal fossa, you have to play with your cleat positioning if your saddle height is correct.

The 109% fit approach would be from the axle of the pedal at it's lowest/furthest stroke (not 90° from bottom). I fit bikes professionally, and I find the goniometer to work best (knee angle 27-37°) because it takes the factor of femur & tibia bone lengths. Now, to get this accurately you need to observe your pedaling style (heel height). You also need to be measuring the shorter of your legs.

P.S. The heel to pedal method is only for a bike shop setting someone up for a test ride.