I've done two of these shops in my area. I was thrilled when I saw them on the job board of an MSC that I signed up with recently. I donate all of our unwanted items to Goodwill several times per year and I also like shopping there because I know my money is going to a good cause. Honestly, I was surprised that a non-profit uses mystery shopping, but it really does make sense. The better their customer service, the more donations they will receive and the more successful their stores will be at generating revenue to support their programs.
In the guidelines for that MSC I shopped for, I believe it says to scan the purchase and donation receipt side-by-side.
Stck, I'm afraid you were misinformed. Goodwill is not a franchise. Its a non-profit organization that has regional chapters and local stores to support the work in that community. The money they make by selling donated items helps fund their programs. So you can't buy into and operate a Goodwill store like a McDonald's for example. The store is run by the organization itself.
I hope this helps!