I'm not sure how they charge on bulk orders, but for a single keyboard, you can do a custom layout for $20. I did that to a Customizer 101 to get a UNIX layout, and as a result of not caring about the caps lock key, I moved that to where ESC normally is, and put windows keys in the normal locations of control (bottom corners). Those 3 keys are blank, as well.
So, 101 with windows keys, in the HHKB (sun type 3) layout for only $20 extra? Score!
So what I'm saying is, if you're buying large quantities of boards, but want something custom, it would be relatively cheap to do. I loves unicomp. A great Kentucky company, too.