In the 1970s I lived near 3 large cities, several smaller ones and a few rural towns. They all had Goodwill stores. I noticed price differences too and asked about it. They said the policy is to price according to location. So if the store is in a well-to-do part of town, the prices are higher.
I can understand this since they are trying to raise money for the disabled.
When I shopped in the well-to-do locations I found NICE clothes with the tags still on them for $10 or less. So I really couldn't complain.