I did some research on VDC and found it has nothing to do with the trans, It is entirely in the ABS system. That explains why a non-VDC and VDC car of the same year have the same trans part number.
Failed TCMs are swapped with identical TCMs with no problems so I took a chance that swapping in a 2006 TCM would work. It did!
My 2005 3.0R with VDC now has a 5EAT transmission and TCM from 2006 LL Beans with no VDC. Everything is working fine now including the VDC, traction control, and sport mode. There are no errors in the ECM or TCM.
Hopefully this will be useful to anyone else who finds themselves needing a transmission but can't find the right year.