As others have said, there is a lot of overlap in the genres compared to other genres: they take place in another world (in one sense or another) where different rules apply. And, most importantly for bookstores, a lot of people read both.
(And I don't think it's quite accurate to say that they are "lumped" together: they may be shelved together or advertised together, but they are still distinct and - with a few edge cases - people can pretty easily identify what is what).
Mysteries and Thrillers are often put together for the same reasons, even though there aren't many similarities between Miss Marple and Jason Bourne.
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