I did a little digging. Keep in mind that the part numbers listed all show the gearbox as remanufactured, so I do not know if the original part number matches the remanufactured part number.
To get a baseline, I checked a 2003 330 and a 2005 330 to make sure they used the same transmission. They do:
Getrag GS6-37BZ - THEG
P/N: 23007532498
The 2006 E90 330i uses:
GS6-37BZ - TJEP
P/N: 23007565853
The 2006 E9x 325i and 2007-2011 E9x 328i uses:
GS6-17BG - TAPX
P/N: 23007626310
For the 2007-2010 E9x 335i's with the N54 engine:
GS6-53DZ - THGX
23007571423
For 2010-2013 E9x 335i's with the N55 engine:
GS6-45BZ - THD4
P/N: 23007599342
*phew* Damn that took a lot longer than I thought.
In short, the part numbers are different for all E90 models compared to an E46. That doesn't mean they won't work, that's just the numbers. Do the research to see if those part numbers have been used before in an E46.