When you swap in a different rear axle and plan to use the stock rear shaft, you do have to take into account the difference in the location of the rear ds joint. That's because the rear ds has a given length. It slips in/out off the end of the tcase output shaft. The slip itself is 3-4" long. The more length in contact through the slip teeth, the more surface area contact, the less potential for vibrations and breakage.
When I did my 8.8 in my TJ, I moved it as far back as possible. You can't get a finger between its diff cover and the gas tank, but there is a gap. Then when I added my stock rear ds, I added the flange necessary to bolt to the pinion flange of the 8.8. Installing it, I looked at the amount of travel on the output shaft of the tcase from the slip. I had just over an 1" which was little more than stock spacing. So I accepted it.