I just did some messing with everything, and here is how we stand.
Standard knee: seems to be to scale, and everything is facing the direction it should be.
Grenadier knee: seems to be to scale, the front of the knee is facing down when loaded into pep
(no big deal)
Gungnir knee: seems to be to scale, everything is facing the direction that it should be
FJ/Para knee: seems to be to scale, everything is facing the direction that it should be
For the models that are showing as being far too large, I tried auto-unfolding at the standard 100mm height, imported the original shin model, and the scale difference was reflected. It seems to be that way regardless of the unfold height. However, as FR already stated, when you go to build it, as long as you have your desired height entered correctly, that is really all that should matter.
-Matt