For those of us who do read BL, we know well enough what "yaoi" means, so it's not, practically speaking, an issue (though occasionally the uninitiated do get blindsided, which is a minor issue. I think mangadex said it's ultimately going to move to "BL"/"GL" tags and content-maturity ratings, so presumably this will sort itself out later on).
Anyway, I've always assumed it's sort of tacit ceasefire situation wherein the target audience for yaoi (fujoshi) would feel fairly uncomfortable looking at even the covers of hentai (moreso than average men looking at yaoi covers, to whom the common reaction is just something along the lines of "ew that's disgusting haha"), and the main target audience for hentai (mostly men) doesn't really overmuch want to see yaoi in their hentai feed and also don't read it enough to realize just how pornographic the un-flagged stuff all is (for instance, I've tried to explain exactly what you just said to the admins of this site before, and I definitely felt they just did not comprehend or believe what I was saying).