Bellhousing bolt patterns are different, so it will depend (at least in part) on whether the transmission(s) in question have removable or integral bellhousings. I wouldn't be surprised if the input shaft is different as well.
What transmission(s) are we talking about? I know I've heard of many people who rebuild their V6 M5OD with the internals from a 4 cylinder M5OD, because the 4 cylinder version uses a lower 1st gear ratio.
If A4LD, the 4.0 L A4LD's reportedly have stronger internals than the others, so, even if you figure out the bellhousing, a 4 cylinder A4LD isn't going to hold up too well to the 4.0.