You see this is where the HHKB falls down. Not when doing simple arrow presses. But when doing more complicated real-world combinations. The simple elegance of the HHKB suddenly becomes a challenging finger gymnastic exercise.
I never realized that you were supposed to use the right arrows with your right pinky on the Fn key. That does look pretty cool, but it does present another problem.
It's slightly awkward to use your pinky finger and press another key at the same time. This is because your pinky and whatever finger you're going to use to strike another key share some muscles in common so you can't completely isolate a pinky movement from your other fingers.
Try to do a "pinky curl" against resistance, but keep the rest of your fingers totally relaxed... nearly impossible. Try to do it, but keep your thumb relaxed. You can do it with a little practice.
Your thumb doesn't share any muscles with your pinky nor does it share any muscles with any of your four fingers so if you use it as the holder of the modifier key, you have greater range of movement and should also have lower muscle tension in your hand at the same time.
The only problem is that the only modifier key the thumb can hit comfortably is the Alt key or whatever key you have next to the spacebar and it you have to curl your thumb underneath a little to keep it held down.
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Having the Fn key there is actually a pretty good move for the arrow keys. Of course, it makes the middle part of the keyboard torture to reach and any benefits you get from splitting your modifier key holder from your fingers would be lost for any middle of the keyboard reaches.