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.