1lum1nat1, there is still the gearbox clutches that can be done, as well as the Torque converter, gearbox oil pressure pump, internal sensors, and some other bits as well, they havnt begun to play
But thats why I think the guys charge 15k to cover for what else could go wrong/having to take the box in/out 5 times all of those good things, but yes I agree with you, manual swap, but good luck in sorting out your box and I hope they do it soon.
The only thing that destroys a manual box is torque overload (spinning the crap out of it on a dirt road is a good example), running out of oil/oil leak, manufacturing defect, or breakage of clips that keep the gears in place, but thats unlikely.
And while clutches are annoying in traffic, your fine german luxury car has got a sliky smooth box, hyraulically assisted clutch pedal, try driving a Mk1 Golf in traffic and see how that one works out for you