I'd imagine the intent with storage is to use the Thunderbolt ports to connect to a storage device (probably one with hardware RAID) that takes up far more phys

I'd imagine the intent with storage is to use the Thunderbolt ports to connect to a storage device (probably one with hardware RAID) that takes up far more physical space than is available inside the Mac Pro chassis itself and has far larger capacity / redundancy that they couldn't fit into the form factor reasonably.