Sorry to hear of your misfortune.
Unfortunately you have now learned the difference between a mechanic,
and a muffler shop artist.

Muffler shops do a sort of freeform art that can be very cost
effective, flexible and practical in some cases. Vanagons are rarely
such a case.

Mechanics replace parts and don't expect the next mechanic to use a
welder to replace them again.

A good Vanagon mechanic replaces parts and also understands why they
are doing things the way they are.

I love my muffler shop when I need a quick and cheap cat replacement,
but he still doesn't understand that you can't mount a muffler
bracket to the body.
For that I have a MIG welder at home to finish the job.

If it doesn't leak then I would just correct the mounting and wait
for the next major repair to worry about the rest. Stud holes are
easier to weld and replace when it's apart for the occasional head
repair which seems to happen pretty often on the boxers anyway.

--
  -Otmar-
82/86 Stretch Vanagon Westfalia GTI. "Power of two" Soon to be TDI.
http://www.evcl.com/vw
1 914 EV, 1 Insight Hybrid