(And past crossovers aren't enough to stop references. The lead character of In Plain Sight cameoed on Law & Order: Criminal Intent before the show aired; but my understanding is that the writers of IPS later made reference to Law & Order as a TV show.)
This one is actually pretty easy to reconcile. The original
L&O was a tv show in the
In Plain Sight universe, it just never had a spin off called
Criminal Intent.
Except that one of the regulars on CI for a few years was a former L&O regular, and there were a number of crossovers among the various L&O series. If one was real, they all were. If one was fictional, they all were. (With the exception of
Law & Order: UK, whose episodes are all loose remakes of episodes from the original, and thus it presumably constitutes an alternate universe.)
Of course, it's possible that in the universe shared by the L&O series and
In Plain Sight, there is a fictional series called
Law & Order that's about something entirely different from the L&O franchise of our universe. Although that would only work if the IPS episode referenced the title of the show and nothing else.)
Anyway, bottom line thanks to the connection between the past thanks to Benny and the future thanks to Sisko there could have been Star Trek and anyone in the future who remembers it probably would not remember much and would just shrug off any similarities as mere coincidence.
But there was no real Benny Russell. The Benny Russell visions were clearly metaphors, fantasies. The second one was a trick by the Pah-wraiths to make Sisko lose faith in his sanity and purpose, and personally I think the first one was too.
I've never been a fan of those old '70s and '80s TV episodes where the heroes debunked a supernatural hoax but then there was a final gag that hinted "maybe it's real after all, woooo."
I've been rewatching
Quantum Leap lately, and this tendency has annoyed me in a similar way. Just off the top of my head, the series managed to imply the existence of alien abductions, ghosts, guardian angels, and vampires.
Well, that's different, because despite its pseudo-sciencey premise and title, QL is a fantasy through and through. Its lead characters' journeys are implied to be the work of divine forces ("God or Fate or whatever"). It's not at all the same as a supposedly real-world, rationalist series like
MacGyver hedging on the debunkings.