The NA and TT have the same 5 speed transmission model #, same splines on input and output shafts, etc. and the housings are the same except for one small difference. The spot where the starter mounts on the bellhousing on the TT is machined a little differently so that the starter will properly engage the slightly larger diameter flywheel and so that the flywheel teeth won’t scrape the inside of the bellhousing. You can use an NA 5 speed in a TT but you just have to shim the starter out a little with some flat washers and sometimes grind a little out of the inside of the bellhousing so the TT flywheel will fit inside. If trying to use a TT trans in an NA you would either have to grind down where the starter mounts so that it could engage the smaller NA flywheel or just use the TT flywheel, which could be used with only a TT clutch. The internals are the same between the NA and TT 5 sp transmissions, although all the 94 + models had redesigned stronger internals. We have used them interchangeably without problems.
The automatic transmission is different for a TT, but the NA auto would still fit in place behind the TT engine, but probably wouldn’t last long. They are different lengths and you would have to use the corresponding driveshaft. Both autos are geared virtually the same but the TT one is built for heavier duty.

(Taken from above link)