Not sure about your gaming stores but around here everything is neatly displayed with covers of the core books facing out to give you a hint as to where you begin and they keep the various games together.
It sounds like you have a well organized FLGS, but with the increasing rarity of gaming stores in general I suspect having a well organized FLGS nearby is the exception rather than the rule for most potential consumers. I haven't been into the only gaming store in my town in several months, last time I was in there all of the Pathfinder RPG stuff was packed into a very small section of shelving. If I remember correctly, the Pathfinder Card Game actually had more shelf space dedicated to it than the entire Pathfinder RPG line. Most of the FLGS space is dedicated to miniatures games like Warhammer 40k, and my impression of the people working in the shop is their interests are more in miniatures games and CCGs than RPGs. I don't even know of a game store in the city where I work (about an hour from where I live), and it is the largest city within a couple hour drive. Most players I know locally order their RPG stuff online due to a lack of places to shop.
When I go to Amazon and search for Pathfinder RPG, the Beginner Box is the 10th entry, behind 6 other Pathfinder products and even behind the D&D 5e PHB, DMG, and MM. The Core Rulebook isn't even on the first page of results (it is on page 2, at spot 26 overall). I went to the Paizo site, and the default view on the Pathfinder Roleplaying Game doesn't even list the Core Rulebook or Beginner Box first; the core rulebook is third (behind the ongoing subscription and the Bonus Bestiary) and the Beginner Box is 11th, behind a bunch of the splatbooks like the APG, Bestiary, Bestiary 2, Ultimate Magic, and Ultimate Combat. They do mention the Core Rulebook in the text at the top of the page, emphasizing that it is 576 pages and that the GM will also want the Bestiary (described as "a massive tome"), neither of which sounds very inviting to new players.
When I search for Dungeons & Dragons on Amazon, the PHB is the #1 result, and the Starter Set is #3. That is without even mentioning the edition in the search. I don't have to sift through dozens of supplements and splatbooks to find where to start.