They're not really separate categories at the retail level unless a store is willing to put a lot of effort into maintaining the separation and dealing with confused customers and lost sales because people are having more trouble finding their books, not less.
This is the problem in a nutshell. With so many authors who write both SF and F, it would get confusing. Not to mention books that some people think are SF and some insist are fantasy, like the
Dragonriders of Pern or some of Vance's stuff (not that he's likely out at B&N anymore), or even the
Star Wars novels.
Bookstores that specialize in SF and F and have huge inventories can probably separate into the two genres, even numerous subgenres. But the fact that there are certain stores that specialize in SF
and F (but not just one or the other) shows that the two are closely allied. And most imprints that do SF also do fantasy.
I've noticed re the recent eruptions between different fanships within SF and F, with a complaint by some made by some that if they buy a book with a rocket ship on the cover, that they expect a fast-paced "lazerbeam pewpewpew" story and not a challenging, diverse story that deconstructs gender expectations or, eeeeeew, one that has romantic arcs. I'm wondering if SFF imprints adopting different "lines" the way romance has might make some of these people happy (assuming any of their complaints about more complex, diverse themes in SF are based on taste and not purely political).
But SFF publishers have resisted this approach thus far, and anyway, many stories blur the lines even within categories like "high fantasy" or "low fantasy" or "urban" vs "contemporary" or "space opera" or "MilSF" or "social SF" or "soft SF." Once you start splitting, where does it stop? And how do you deal with books that contain elements of more than one subgenre without becoming prescriptive?
I personally wouldn't like it if the already paltry SF and F section at our local bookstores was compartmentalized into smaller sections based on someone else's perception of where various titles belong. Though I've pretty much given up on finding much at the local B&N anyway. They don't keep even new titles by less famous authors up on their shelves, and they don't carry much back list, even for more famous ones. It's no good for discovering writers I haven't heard of before, and it's frustrating to find the most recent release in some series I haven't read but looks interesting, and the earlier books in said series aren't stocked.