Actually, the 2009 you have uses a few different transmission ID part numbers, depending on engine, transmission, transmission / vehicle production date, wheelbase, PTO / non-PTO, possibly other options, and these variations in mechanicals have less to do with Thor (the coachwork / conversion company), and more to do with the E350-cutaway chassis built by Ford. The only way I could see this being legit is if the trans in the bus is not the correct ID tag for the engine it has, not likely. Fords are very specific per vehicle in production, and an incorrect trans is not likely to operate correctly, or for very long, if it even operates at all.
Your 2009 should be new enough that a simple call to a Ford dealer parts department can tell you (from the dash VIN for the cutaway chassis built by Ford) which transmission version ID tag is correct. That can then be compared to the one currently in it. Which is something that the shop should have done, and that you can do yourself. Secondary verification with production date on the manufacturer's label in the driver's door jamb may be necessary, but not likely.
The following from car-part.com (downloadable screenshot attachment end of my post) indicates these transmissions are very specific to a vehicle's production date and equipment. Without the production date or cutaway chassis VIN, I cannot guarantee that your exact one will be here, as it is possible a late 2008 could be titled as 2009 or have 2009 parts, early 2009s could be titled as 2009 with 2008 parts, a late 2009 could have 2010 parts, or an early 2010 could be titled as a 2009. Ford has a history of designating such models "xxxx - 1/2" models.
2009 Ford Van E350
AT, 4R75E transmission, (8-330 5.4L), ID 9C2P-DA
AT, 4R75E transmission, (8-330 5.4L), ID 9C2P-DB
AT, 5R110W (TorqShift) transmission, 10-415 (6.8L), 138" WB, from 12/01/08, (ID 9C3P-GB)
AT, 5R110W (TorqShift) transmission, 10-415 (6.8L), 138" WB, thru 11/30/08, (ID 9C3P-GA)
AT, 5R110W (TorqShift) transmission, 10-415 (6.8L), 158" WB, from 12/01/08, (ID 9C3P-HB)
AT, 5R110W (TorqShift) transmission, 10-415 (6.8L), 158" WB, thru 11/30/08, (ID 9C3P-HA)
AT, 5R110W (TorqShift) transmission, 10-415 (6.8L), 176" WB, from 12/01/08, (ID 9C3P-HB)
AT, 5R110W (TorqShift) transmission, 10-415 (6.8L), 176" WB, thru 11/30/08, (ID 9C3P-HA)
AT, 5R110W (TorqShift) transmission, 8-330 (5.4L), 138" WB, from 12/01/08, (ID 9C3P-EB)
AT, 5R110W (TorqShift) transmission, 8-330 (5.4L), 138" WB, thru 11/30/08, (ID 9C3P-EA)
AT, 5R110W (TorqShift) transmission, 8-330 (5.4L), 158" WB, from 12/01/08, (ID 9C3P-FB)
AT, 5R110W (TorqShift) transmission, 8-330 (5.4L), 158" WB, thru 11/30/08, (ID 9C3P-FA)
AT, 5R110W (TorqShift) transmission, 8-330 (5.4L), 176" WB, from 12/01/08, (ID 9C3P-FB)
AT, 5R110W (TorqShift) transmission, 8-330 (5.4L), 176" WB, thru 11/30/08, (ID 9C3P-FA)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 138" WB, from 12/01/08, PTO, (ID 9C2P-EB)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 138" WB, from 12/01/08, w/o PTO; (ID 9C2P-AB)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 138" WB, thru 11/30/08, PTO, (ID 9C2P-EA)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 138" WB, thru 11/30/08, w/o PTO; (ID 9C2P-AA)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 158" WB, from 12/01/08, PTO, (ID 9C2P-FB)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 158" WB, from 12/01/08, w/o PTO; (ID 9C2P-BB)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 158" WB, thru 11/30/08, PTO, (ID 9C2P-FA)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 158" WB, thru 11/30/08, w/o PTO; (ID 9C2P-BA)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 176" WB, from 12/01/08, PTO, (ID 9C2P-FB)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 176" WB, from 12/01/08, w/o PTO; (ID 9C2P-BB)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 176" WB, thru 11/30/08, PTO, (ID 9C2P-FA)
AT, 5R110W (TorqShift) transmission, 8-366 (6.0L, diesel), 176" WB, thru 11/30/08, w/o PTO; (ID 9C2P-BA)
Unless the dealer comes back with a trans ID different from the one currently in it, there's simply no way to prove originality. Possible the shop took this step and that's what they found, but if so, they should have explained that to you. Even if it were swapped, as I said earlier, there's probably only one version that will fit and operate correctly, because Ford is constantly revising things like shift programming and line pressures, solenoids. A vehicle that new with an incorrect transmission will usually let you know pretty quick, especially a Ford. You couldn't even get away with that in the 90s. I know someone who took a '97 P71 trans and put it into a '96 P71. Fried it in 30 days, and you could smell transmission fluid the whole time it was burning up. So it IS possible, but it couldn't have been in there very long.
I will extend the shop a little leeway here and say that it's not their fault if the trans was indeed not the correct unit. But while there may have been nothing they could do immediately other than replace the seal to stop the leak, if the transmission was indeed the incorrect one, it wasn't very responsible or professional to do so, if they knew it was not the right transmission. If I could prove beyond a reasonable doubt that the transmission was not the correct unit and prove this to the owner, I would have tried to persuade them to get a correct used unit, not just slap another seal back in it and hope for the best.
IF the dealer can't help you (unlikely), you might trying running the VIN through
www.compnine.com -- no guarantees on an incomplete chassis, however.
car-part.com screenshot: