I feel the most comfortable positions for Fn keys on the HHKB should be the traditional location of 'Alt' and 'Alt Gr'. The right-pinky on Fn design is not very convenient in my opinion, because I don't want to move away from the home row AND home column too much, and this right Fn has some problem.:
1. It's more natural to do thumb-Fn and middle-Tilde.
I flipped the DIP switch to make the original Delete to BS, and for Delete, I don't feel too natural to use pinky-Fn and then hit the top right corner key (Backtick/Tilde) with my index/middle finger.
2. To use the default navigation cluster designed by HHKB, one definitely has to move away from the home column.
One doesn't need to move away from the home row much on a 60% keyboard but to reach for the Fn key next to the R_Shift, there are two ways: twisting the wrist to the right or moving the position of the whole right wrist by 3+ columns. Twisting wrist is good because there's no need to look for the home column position again: you just twist you right wrist back. Moving wrist is bad because to get back to the home column position after reaching for the right Fn key, one has to search for the homing J key, and it is slow to reach by move the whole wrist. It is possible to use just the twist wrist method for the F1-F12 function keys, however, to use the default navigation cluster designed by HHKB, one has to move his right wrist, and twisting is not an option.
If I redesign the layout, there'll be two Fn keys and they will be either the pair of inner modifiers or outter modifiers on the space bar row. I can use the Fn key next to R_Shift for Windows key and 'Super' or other things in Linux. And I would remap the nav cluster to somewhere like WASD / IJKL / HJKL where I can use my thumbs to press Fn key and have my hands stay at the home row and home column.
HHKB JP is much better designed. Japan is a country where the best products are reserved for the countrymen. Look at the 0.25u gaps separating the left Fn and the nav cluster - yes, they have a nav cluster. It is just the unsolvable R_Shift problem if they include a nav cluster in such a small keyboard, and that not all users can get used to the ISO Enter.
Otherwise, the location of Fn key next to R_Shift is actually the perfect location for the upper arrow key in other form factors, e.g. 75%, 65%, 68%, the Cherry 1800.
P.s. I do kind of hardcore touch typing 50% of the time on HHKB2, i.e. I use blank black caps and I put the HHKB in a dark "keyboard drawer" and when I type, I put my hands inside this "keyboard drawer" to type.
