I know nothin' from nothin' about Bays... but ...
I expect the manual Bay trannies are more or less the same as the early air-cooled Vanagon manual transmissions. I'm making this guess on the basis that late Bays had much the same air-cooled engines as early a/c Vanagons. I'm also guessing that the Bay auto trans is also much the same as the Vanagon A/T.
Air-cooled Vanagon manual transmissions are highly sought-after by the inline-4 conversion crowd, because they have a higher final drive than the factory diesel manual Vanagon transmission, which is geared insanely low. A lot of I4 conversion people want to use the original Vanagon diesel engine mounting for their new gas or diesel VW I4, because they can mount the engine on its side at 50 degrees. But they can't stand the low gearing on the original diesel manual trans, so they want to ditch the diesel trans.
The air-cooled manual trans will bolt up to the rest of the 50-degree mounting hardware for people who go I4 with scavenged Vanagon diesel parts. The big advantage of the original diesel mount is it lets people lay their engine over on its side, at about a 50 degree angle, so the engine cover doesn't have to be hacked up for clearance, intruding on the folding bed cushions.
However, I seem to remember that you can't use the Vanagon automatic transmission with the 50 degree engine setup. So I doubt you could use a Bay AT with the 50 degree mount, either.
I think Vanagon drivers who want to stick with their slushbox have to go with a 15 degree engine mounting, and a Kennedy Engineering adapter. The engine stands upright, like in the VW cars, rather than on its side, like the factory diesel Vanagon. If you intend to run a turbodiesel, then this will make the oil drain line from the turbo easy ... just stick with the car setup completely, from valve cover down to oil pan. Rigging a turbo oil drain with the 50 degree setup can be tricky, as the original 1.6 NA Vanagon engine didn't have any provision for that, and it already has a funky special oil pan & dipstick that you have to move to the new engine when you lay it on its side.
There's a guy in Canada who sells a complete 15 degree kit with all the bits & pieces, and he has a photo up of an auto-trans Vanagon as an example vehicle -
www.fastforward.ca. That would save you a lot of hassle, assuming the parts fit Bays. Very expensive, though, relative to buying used Vanagon diesel parts at a wrecker. But if you stay slushbox, I don't think you have many other options.
I would try asking this question on TheSamba, as I expect there are more people over there who have converted their Bays to I4 - maybe even a few slushbox owners. Also, check
http://autos.groups.yahoo.com/group/TDI-conversion/ to get in on discussions about Vanagon I4 conversions - maybe some Bay people there, too. Anything can be done if you spend enough money!