Honestly, all the small shops have to do to stay in business is offer something the big guys or internet can't - SERVICE. As you said, your local PRS vendor isn't going to have an issue as they have the agreement with PRS to carry the Core and higher end stuff. The two smaller chains mentioned need to up their service game. None of them can compete with internet pricing so they have to take a cut on the profit of movable goods. Where they can make up for it is in after sales support.
Take a setup for example. Say a setup costs $30, done by a person who listens to what you want, is excellent at what they do, and can turn it around same day. This shop will have heavy foot traffic and will probably need to hire another guy or two to keep up with demand. At the same time, musicians will drop money on stings, picks, and other inexpensive items. Add in the fact that a shop like this will restring and setup every guitar that comes in (new or used) before it goes on the floor (and adjust it for the purchaser), you have a shop that will succeed. Guitar Center typically doesn't do these things.
It's sad, but Guitar Center is not a place I think of when considering high dollar guitars and gear. At least not where I am. For online sales, I'd rather buy a new or used PRS from an authorized dealer such as Dave's or Sweetwater. Why? They get the service part. For example, I know that Sweetwater sets up every guitar before it leaves the warehouse. I also know from experience, that when ordering a new guitar, you can request that they change the strings from 9s to 10s and then set it up. That's service. Guitar Center will let you walk out the door with a guitar already needing a string change and a setup.
I do like GC for certain things. But they aren't in the same league as the mom and pop shops. You are propably going to see a store that wants to compete in the mid range level. Lots of SE's, ESP LTDs, Epiphones, base model Gibsons, MIM Strats, etc. Nothing wrong with that. They are going after a certain segment of the market. But they can't offer the "after the sale" support that a mom and pop can and should.
Sorry for the rant......hahaha