I realize that, and am not trying to argue that point. I just used it as illustration. The changes I mentioned in the ST3 novelization would not have changed the actual film, even had they been added. And as you stated, even the difference in Kirk's death would not have really changed the film. They only changed it for audience perception, because most audiences cannot understand the poetic justice of Starfleet's greatest hero dying in such an ignominious fashion.
The point is, even Paramount cannot decide on the rules or implementation of its own canon. Say what you will about Lucas' huge control of the Star Wars franchise, at least he keeps it in pretty good order. If Paramount is to revive Star Trek to its previous popularity levels, the first thing they must do is appoint a sitting executive or "council" to oversee the direction of all facets of the ST franchise. Roddenberry, Harve Bennett, and Rick Berman have all filled this type of post. It was when ST was turned over to the bean-counters that it failed so utterly.