Besides, it's probably hard to find a modern SFTV series that doesn't have characters making references to Star Trek as a fictional series at some point. I don't recall if there were any in Alphas, but I'd be surprised if there weren't.
Star Trek is a hard one, because it is so pervasive in pop culture.
I ran into the same problem when trying to define my own personal continuity for the X-Files and which series I could include as sharing that same universe. Lone Gunmen and Millenium were easy no-brainers and Fringe went out of its way to include itself in the X-Files' world, but I really wanted to insert Supernatural into this continuity out of a personal preference on my part. Problem being, in the pilot episode of Supernatural, a couple of extras call the main characters "Mulder and Scully" and over the course of the series, references to Mulder and/or Scully have been rampant.
My go-to fix for this sort of continuity problem is the X-Files episode "Hollywood AD." In this episode, a movie studio makes a film called "The Lazarus Bowl" with Garry Shandling and Tea Leoni playing characters named "Mulder" and "Scully" respectively. From this, I just imagine that the movie became a huge hit in this universe, enough of a hit for people to reference, and I can now include Supernatural and many other shows or movies that name drop Mulder/Scully without much hand waving at all.
Off hand, I can't remember a Trek episode that could explain away in-universe references to "beam me up" or "Vulcan neck grips" in the modern day of the Trekverse. Was there any mention of a "Trek-like" TV show in Greg Cox's Eugenics Wars series?