If AJA says Slot 3 is optimal, you should install it into Slot 3. Those folks spend a LOT of time testing all this stuff for us and I always follow their instructions to a T. Including the Expansion Slot utility.
the slots in the Mac Pro are dynamic, and the number of lanes can be changed with the apple Expansion Slot Utility. Slot 3 is the "safe" slot, as you can't screw it up (by making it a 1 lane slot). Everything depends on where you put your storage host card (SATA, Fibre, or SCSI).