The DIP switch can set the curser (arrow) keys to additional mods and r-shift, but the Jp keys are pretty much useless for non Jp writing. Maybe with a keymapper software they can?
It was my concern before buying one: I think the main point why non-japanese people do buy the HHKB Pro JP is precisely because they want to use these keys left and right of the (tiny) space bar as modifiers (at least that's why I wanted to buy one: so that, thanks to the tiny spacebar, I could reach the keys at the left and right of the spacebar without distorting my thumbs too much).
So before buying one I asked here on GH if someone had already remapped the "japanese" keys of an HHKB Pro JP to act as alt / super / hyper / you-name-it and nobody answered... But I figured out that it would very probably work so I had one sent to me from Japan.
And I can tell you that remapping worked like a charm
I don't care about what's written on the keys: I started with a US layout and simply checked which key is sending which keycode and configured my system accordingly. For example the key physically at the left of the spacebar is ALT and I configured the key at the left of that key to be the "Super" modifier.
I'm working exclusively on Linux and remapping on Linux is easy... I take it it would work on Windows on OS X too !?