Upon discovering that Boimler's holodeck program features time travel as a plot element, Mariner states that she hopes the story line doesn't involve going back in time and assassinating former US President Kennedy. A story line involving the crew of the original Enterprise traveling back to the 1960s and being forced to assassinate President Kennedy had been repeatedly floated by series creator Gene Roddenberry for various Star Trek revivals. According to some reports, his insistence on such a plot line for a sequel to Star Trek: The Motion Picture (1979) was one of the major factors that led to his removal from that project.
Boimler finding that Ki Ty Ha is really the "Wright Flyer, Kitty Hawk, NC 1903" (referring the plane of the first flight in history made by Orville and Wilbur Wright in Kitty Hawk bay) is similar to how the Enterprise found that V'Ger was really "Voyager VI" in Star Trek: The Motion Picture (1979).
References the events of the Kelvin timeline movies: at the beginning of the holodeck program, Mariner complains about Boimler potentially piggybacking off of her version of that program. When he tells her that he hasn't, she says that she hopes this isn't some kind of "alternate timeline concurrent to our own but with people who look slightly different and are younger than us", which is the basic set up of Star Trek (2009).