Very good question.
In my experience, most stores associate low arches, flat feet, and/or high level pronation with having bad feet and needing lots of correction. This is how it goes:
-Because most humans pronate to a noticable degree, they will say that they need to stability/support/control in their shoes or they're going to have problems, and possibly a Superfeet too, for an extra $29.95.
-And then the people that have rigid arches/minimal subtalar joint movement are told that their foot has very little pronation and consequently very little "natural shock absorbsion" and therefore needs lots of cushioning because their foot is so stiff.
Often they'll just have you take off your shoes, squat in plact and see what the subtalar joint does. Then they'll bring out either neutral, stability or motion control shoes and have you try them on you tell them which feels best. You'll probably run in them, but will be lucky if they actaully watch you run. The funny thing that 90% of RSA employees (most of them are probably HS or college students. You get some who are adults who know a thing or two, btu often what they know is so intertwined with believing that the technology is everything thatyou'll just get the "this shoe is what you need" speech) will see you do your squate and will be looking at your feet, but not realize that your pronation, whatever it is, is allowing your knees and toes to line up just right -- that's what it's there for.
They think that your foot is incapable of running on it's own without problems -- whether your a higher level pronator (and need lots of control and support) or a low-end pronator (and needs lots of cushioning).
My approach is that your feet are generally fine on their own and it takes a shoe to screw them up. My job is to get you a shoe that doesn't cause any problems and allows your foot to ride the same in the shoe as it would if it were barefoot.
Last night I had a kid from Mt. SAC that I was working with -- fast kid (21.x for 200m) who was picking up someo spikes but was having terrible shin splits when he was doing his general running. I tried him in some shoes, and the 900 and Nike Free felt best because they weren't interfering with his foot -- his old shoes were clunkers. Most stores would hear "shin splints" and either automatically start with the Adrenaline/Addiction, and/or bring out the orthotic. Guys, there's probably nothing wrong with his feet, and everything wrong with his shoes.
So that's your explanation in a nutshell.