Yes I have noticed it, and I disagree with it. It existed for the very reason of not angering the fan of the different series by doing things just as they didn't with Admiral Janeway. Also it existed to help keep the canon (tv series, and movies) & non Canon (books) for having major conflicting storylines.
You are incorrect.
Those Submission Guidelines aren't ever aimed at the regular stable of ST authors, and never were. They are only aimed at first-time, would-be ST authors, so they can prove to Simon & Schuster and Pocket's editors that they can follow instructions and craft a ST story that reflects only canonical ST.
But if/when one your novel proposal is accepted, you can negotiate with the editors and CBS Licensing on any plot elements that might deviate from the guidelines you had to follow to get the right to pitch.
Again, incorrect. In one ST novel series, Nurse Ogawa has an only child, a girl. In a different ST novel series, she has an only child, a boy.Any new non canon written from this point out now has to work with these non canon changes instead of being able to create works from within the established canon because if they do they cause conflict to the non canon.
Ensign Rager, now promoted, is seemingly serving on two starships at the same time.
"Crucible: McCoy" and "Crucible: Spock" deliberately ignore many other ST novels.
Admiral Janeway is alive and well in the Shatnerverse novels and the new "Star Trek Online" novel tie-in.