The threaded bolt holes in the floor of the cargo area were intended for a row of seats- they're certainly up to the task of holding down a spare tire, IMO.
What's wrong with underneath the cargo area though? a 33" tire fits down there, and when you raise that cross member it's out of harm's way, protected by your receiver hitch. I too wouldn't want to give up that interior space.
99 uzj100, gx470
05 525EXC, 01 XT225, 07 TTR90, 07 CRF50