It would be hokey not to fill up the 3 memory slots each so that when do a simple power on test at the factory you test all three memory controllers. Leaving one slot empty on each process would skip that minimal testing.
Same reason don't ship boxes with no ram and no disk. You'd have to put in the ram/disk , test, and then take it out again before final box/ship of the device. It is simpler manufacturing process if don't remove things from the box as it goes down the line.
So it is either going to be 3 memory slots filled per processor with 1GB or 2 GB DIMMs. Bumping up to 2 GB DIMMs would cost more than 1GB ones. However, it is a bit lame of Apple because the 2GB DIMMs are around same prices as the older 1GB DIMMs were at this point. Several of the Mac Pro 3rd party memory vendors (OWC, Crucial, etc.) don't even sell 1GB parts anymore.
Will be even more lame when the next gen Xeons come which seem likely to have 4 memory controllers. If Apple is still playing the 1GB game, then it will be 4GB and 8GB respectively as the standard memory. The low end Mac Pro will have at least matched an entry iMac in memory, but with parts can't even buy.
(I'm a student) and then I get the dreaded "Problem with your order" email 
