The tech manual was a best seller for a surprisingly long time and it wasn't til later, around the mid-80's/pre-production of TNG that Gene Roddenberry declared his starship design rules fiat to gank the FJ work. So as of 1979, it was still official Star Trek. So why wouldn't it have been consulted? Especially since they were going for a more grounded and believable feel to the Starfleet stuff, to nicely contrast the more fantastical elements of the V'Ger business. Hence, the authenticity of radio chatter and the pre-flight warp systems check list (straight off of TO:03:11:20 from the TM). The references to the FJ TM in the first couple Trek films should not surprise anyone.
While Data Holmes
's characterization of the matter is a little lacking in objectivity, I agree that back then there was no polarization between "official" work and "fan" work. Heck, there wasn't really very much Star Trek
material out there, period, and it hadn't gotten to the point where portions of the official and licensed material were contradicted by other portions (except for things like the Gold Key comics getting the details of the show hugely wrong). So naturally they were going to draw on whatever supplemental material existed at the time.
It's kind of like the reason Lucasfilm counts all Star Wars
tie-ins: because there really isn't that much screen canon to work with, relatively speaking, so if you want to flesh out the broader universe, it helps to draw on the tie-in material that may have already done so. The FJ manual was an available resource for background material about the Trek universe, and it was one of the only
available resources in existence at the time, so they found it useful to draw on it. There was no thought given to the idea of "canon" at the time; that didn't become a bugaboo in Trekdom until the TNG era. (Although there were some lively debates before then about whether the animated series counted as "real" Trek or not. Some people dismissed it, and lots of people had never seen it.)
I think it's less likely that the makers of the film were under the shroud of ignorance offered the makers of the television series when it came to realizing that fans would spend their lives belaboring every last detail. Fans had already been in the practice of recording episode audio from television broadcasts for use in (over)analysis. The same practice had to be expected of the feature film -- if not when it was in theatres, then when it aired on television, the rights of which had been pre-sold to ABC before the film's box office debut.
Even so, those fans would be a tiny percentage of the movie's audience, and the filmmakers wouldn't change the way they did things just to cater to that small fringe. Even decades later, you still have movies and TV shows recycling old props and putting gibberish or in-jokes in onscreen text and the like.