update
I picked the car up yesterday. Transmission was replaced and emission modification 2A completed. Maybe not my best decision, according to your advice too, but I took the chance.
Car drives well for as little as I got to test it. In D it seems to be shifting at higher points.
The shifting lever catches slightly when taking out of P, it needs to be pushed forward a little first, then the lock button releases more easily. At the end of testing it out yesterday it was not as clunky but still noticeable compared to before the repair.
There is a somewhat high pitch noise (bearing, belt?) from the engine at idle, heard when the hood is up. Not sure if because engine was cold or this happened before and I just didn't notice.
Paperwork indicates that the dealer was advised by VW to replace transmission based on the pictures that the dealer submitted.