While the Gen IV YJ's LS series 5.3 aluminum V8 is shorter and lighter than the OE 258 six and the 6L80 6-speed automatic overdrive transmission is a fraction of an inch shorter than a 4L60, there was still a fit issue.
Yes, the 6L80 is shorter than a 4L60, but it's taller than a 4L60. Motech had to space the transmission mount up in order to keep the 6L80's pan up high enough to be safe in the rocks. One plus -- because of this, the Atlas didn't have to be clocked flat, which meant the floor of the YJ didn't have to be massaged much.
Look closely at the photo. The pan isn't just the brighter aluminum piece the flash reflected on. It continues to the lower right edge of the photo.
There's always something to deal with when it comes to fit.