Good question, I don't trust muffler shop guys to weld much of anything, I'd look for a professional welding shop personally.
I wonder of spraying a good coating of VHT paint down into each pipe would help those iffy areas you mentioned last longer?
Personally I say if it works, bolt it on and ride until it's worn out, then bolt on the next one. I'd keep them as a spare set and think about customizing them after those weak areas fail.
Cheers.
-A