Osiris
Zen MBB Master
Well you know better than me because you have done it. Now that you have said that... it's given me the idea that each knee goes through a different loci of points depending on chainstay. I still suspect the knees will go higher with a higher bottom bearing.
The maximum height of your knee relative to your shoulders is determined by the seat recline angle, the length of your torso, and the length of your femur. None of those variables are changed by raising your feet. Below is an animation of a study I did several years ago. It's purpose was to discover how to set up the pedals in a hypothetical velomobile to obtain the most compact aerodynamic shell. Increasing the height of the pedals naturally resulted in a more open knee angle during maximum flexion, but it had no effect maximum knee height.