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?
There's a Trek-as-TV reference in The Rings of Time, when Zoe speculates about "sexy green girls."
Personally, I like to think that Titan: Synthesis is a covert Transformers crossover. The Sentries believe that FirstGen Zero-One
was destroyed in slipspace, but what if it simply decanted into another universe?
It would immediately cast about for signs of the Null, and, finding none, would produce a batch of SecondGen
, programmed to keep vigilant watch for the destroyer --the physical incarnation of Chaos
. It would then go dormant to conserve power.
Aeons later, this initial programming has drifted into legend and myth, and ultimately the SecondGen turn on themselves in a civil war. . .