It's not as simple as that. Two separate dual core is better than a single dual-dual in some cases because each socket has its own independent bus, offering a lot less opportunities for contention, four cores per FSB, or two cores per FSB. The difference isn't earth shattering, but for many uses, there is a difference.
Other makers allow you to spec out their workstations with only one chip though, so you could just buy one dual-dual core chip and leave the other socket unused, and you can populate the second socket at some other time. One problem with that is that the price of some competing workstations is such that you can get both sockets populated in the Mac Pro for the same price for similar spec chips, just fewer chip choices.
There's probably not much difference in power efficiency because the dies are mostly the same difference, a quad core Clovertown has two Woodcrests stitched together into the same package rather than one each in two separate packages.