I think you would be incorrect on that. If you look at the performance specs of the W9000, the d700 fits nicely within that realm. Apple is assuredly getting a volume discount on the GPU's, probably at lower frequencies, and with the single fan Mac Pro handling the cooling, it isn't a straight equivalent of a PCie card for a PC.
Perhaps, but given that a single W9000 retails here at ~£2700, I cannot see how Apple would be getting such a huge discount to include two of those plus a ~£1300 Xeon chip, not counting the other bits and labour+delivery to retail the package at just below £3800 with "Apple premium" included Even if Apple were getting those parts at 50% cheaper than they cost retail, it still makes no sense...