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.
I do believe that the "introduction to navigation" manual was also used for the navigation data shown on screen in TWOK as well.
Fandom wasn't a dirty word to the studio in those early days. Roddenberry turned sour against the fans a little when they "liked" trek without him more than TMP. So, when he came back to trek "power" with TNG, he was ruled by a hurt ego and the whispers of the forked tongue of his lawyer to lock down control as much as possible. Thus the birthing of "canon" and the disavowment of the fandom tech works, novels, and animated series. It was his trek, or no trek.