Good question, I am not aware of any minimum distance spec. The I/O panel will determine the spacing, as you know.
IMO, as long as any component leads, etc, are not touching the case/tray under the mobo, you are fine. A thin insulator is a good idea, thin being the keyword.
Case design will dictate the size of the standoffs, and not including any with that case is strange, I certainly agree. I've never used a rack style case, are their standoffs shorter? In a standard PC case, the clearance is only a few millimeters.