I just finished building my version of this bench, pretty closely following Benchcrafted's plans but using mostly power tools (and some hand tools). I left the center partition sitting just below the surface of the tops to ensure it couldn't possibly interfere when in the "down" position, and that is working very nicely.
With holdfasts I haven't yet found the need to use clamps through the split, but when the need arises, I'll be happy for it. And, handling the top as two pieces was a BEAST... joined together it would be brutal.