It is hard to believe but true!!
In fact there was a period when it was not possible to use Nikon Capture Control with the D700, an software update to Capture Control rectified this.
It also means you cannot connect the camera to a laptop and xfer the files as I found out in the field one day much to my peril. You need to take the card out and use a card reader.
DPReview's review disagrees. On page 12
the animated GIF at the top shows the USB setting in the Setup Menu. On page 13
To test the D700's USB transfer speed we transferred approximately 420 MB of images (mixed RAW and JPEG) from a Lexar Pro 300x (UDMA) 8GB CF card. In this test the D700 performed fairly well, though you'll still get far faster transfers if you use a good CF card reader.
. This directly contradicts your statement that you can't transfer NEF's directly from the camera.
Capture Control often needs updated to recognize new camera models. And the fact that it worked after they updated shows that the D700 does indeed support MTP/PTP mode. Did you actually check the menu setting I described (also pictured in the DPReview review)?