My best answer is that it shouldn't matter since they actually connect to the transfer case. You could always double check the length, but that would be the only possible difference unless it's a rubicon. I believe they use a different, slightly more heavy duty connection. I'm sure somebody will correct me if I'm wrong.
Thanks to all for replies. I had ordered a used DS (my local rebuilder wanted a small fortune to straighten mine) for my automatic tranny. When it arrived, the paperwork indicated it was for a manual tranny but it was too short. Found a reasonably priced new one on Quadratec’s web site but the description did not indicate if it was for an automatic or manual so I entered into a chat conversation with them and was told there is no difference. I find that hard to believe.
For 2002 and older TJs, the automatic transmission is much wider so the front driveshaft is made with a smaller diameter to clear the transmission. You can use a the smaller diameter automatic transmission style front driveshaft if you have a manual transmission, but you cannot use a manual transmission style larger diameter front driveshaft if you have an automatic transmission.