I think this is where lack of n-key rollover is going to bite a lot of people in the ass. Looking at that list of problem key combos, I bet a lot of matrix designs are simply not capable of doing some of them.
The HHKB lite is a 'normal' rubber dome, not capacitive. It doesn't have NKRO. The fact that it needs the Fn key held down just to make what are normally single key presses makes it especially susceptible to this limitation.
The HHKB Pro has NKRO (within USB limits) and should be fine.