Dick: [...] Now stay with me here, 'cause this is the most Important Part of this whole interview. If you follow the FJ Timeline through 1975 and 1976, Paramount rejects script after script from GR and others, while FJ's Plans and Manual climb the bestseller lists to astronomical heights. GR's head must have been ready to explode. Then, if you read further, Paramount starts to court FJ as a consultant for the movie but FJ declines any involvement. At that point, Paramount and GR have the same problem. Because of the aborted Lincoln Enterprises deal to publish the Plans and the Tech Manual in 1973, and because Lou Mindling of Paramount allowed FJ to copyright the Manual in his own name in 1975, neither GR nor Paramount owns the rights to FJ's original work (such as the Star Fleet space station, the Dreadnought and other ship designs, the UFP "two faces and starfield" logo, etc.). [The rest of this paragraph is pure speculation, but I don't think I'm too far off the mark.] GR doesn't want to use FJ's designs because he feels he has had little control over their creation and no control over their publication, and he'll be damned if he'll pay royalties to an outsider for stuff spun off from the universe he created. Further, FJ has proven difficult to deal with in other encounters (Planet Earth) and GR doesn't want to go through that again. Paramount desperately wants FJ to be involved with the movie because FJ's work is so enormously popular, but FJ is not being a "team player" and agreeing to be a consultant or a writer on the project. If FJ is not going to be directly involved so they can exploit his name in their publicity, then Paramount doesn't want to pay him royalties, either.
After that point, everything in the movies was either designed to directly contradict FJ's work, or to modify designs or concepts first put forward by FJ to make them just different enough that FJ could not claim copyright infringement (especially the UFP logo you mention in
Q12). In retrospect, knowing what a "control freak" GR was about the series and the movies (as documented in many written accounts), none of this is a surprise to me.