I have my HHKB Pro 2 set up with only dip switch 2 up for Mac mode and I have never had any issues with it whatsoever.
As far as protecting it, I just push in the keyboard tray when I'm not using it.
Contact BeNippon or your vendor of choice - I have seen several pictures of clear hard plastic covers that sit over the keys of the HHKB. They are really popular in Japan and they make them for most of the decent keyboards like HHKB, Topre and Filco. Specify you are looking for one for the Pro because there are special ones for the Lite 2 which have a hole cut for the arrow keys.
If you get one from BeNippon, I'll probably order one as well.