A 3-image stitch from a 12mp DX camera will give you more resolution in the final image than a 3-image stitch from a 12mp FX camera, because there will be less overlap between the images. So from a pure resolution point the DX camera wins out for stitching with a T/S lens. You also have the advantage of not using as much of the extreme edge of the image circle.
Also, at least one poster at DPReview has claimed that using shift for stitching does not work well on the D3, at least not with the 24 PC-E (the 45 may be better, I don't know).
I've used the 24 PC-E quite a bit for stitching, and also the 85 PC Micro. I just got my 45 PC-E today and look forward to trying it out this week.