Totally understand your frustration as my OCD would be going mental right now!
I thought as much in regards to the turbo and the waste gate but you’ve already done your homework with the voltage parameters....simple adjustment and you’ll be good there. You can do it yourself with an OBDELEVEN not that you should have to as the vendor should be checking that after refitting the turbo.
you may have landed slightly unlucky with the service from the tuner as you mentioned that they have had some pretty good right ups online, hopefully they do the right thing and rectify the issues.
I can’t stress enough to people the benefit of doing your homework in going with a good tuner, which is probably why I put up with the 16 hr round trip to visit Unicorn in Stockport for my engine and DSG mapping, as it pays off in the aftercare and reliability....after 40k miles with my tune it hasn’t missed a beat.
You’ll be glad when everything is sorted out and your R is back to full health.