The Jatcos have an extra layer of BS on them, and the battery tray actually sits higher due to the extra harness underneath them. Don't have one in front of me, but that hinders the ease of FCM replacement (because on the ALH and manual BEW cars the FCM is cake easy to replace).
Here is a AWW 1.8t engine equipped with the Jatco, the BEW is similar, and you can clearly see that extra harness right over the top of the FCM bolts:
Incidentally, the BEW NBs got the 02E DSG transmission as their automatic option, and I suspect it was because there was simply no room to stuff that giant bloated Jatco transmission in there with regards to how tight it is around the battery area, which on the NB is already extra tight, even with the smaller battery they got. And the AWW/AWP NBs continued with the 01M right up until they switched to the 6sp Aisin unit, which is actually physically smaller than the 5sp Jatco and being that its valve body is on the bottom instead of the front I think that helps.