Since, as I understand it, it was GENE who, around the time of the first movie, declared TAS no longer a part of the timeline
Tough shit on Gene. It aired, it's canon. Even if it sucked (like "Way to Eden," for example.)
Thank you, T'Bonz.
To further cloud the issue is the question of just what exactly did Gene say about TAS and why? He never said a word to Dorothy Fontana, David Gerrold, or Bjo Trimble about any supposed dissatisfaction with TAS (in fact, the Ballantine edition of Bjo's Star Trek Concordance, which features TAS heavily, sat on Roddenberry's desk all through TNG, and at no time, in all the many times she visited the set, did he indicate to Bjo that, should she do an updated version of the tome, to leave TAS out).
Best information points towards the whole matter having to do with the dissolution of Filmation in the late 1980's, and the sorting out of all its licensed properties, including TAS. In short, for legal reasons, writers for TNG, were not allowed to make references to TAS, until the lawyers had their say in determining who had what rights and how much Lou Scheimer and Co. needed to be paid.
By the time of DS9, the matter had been sorted out, TAS was now Paramount's, and the TAS references started seeping in. Sort of a backdoor canonization, if you will.
Besides, David Gerrold puts the whole matter in perspective in the featurette on the DVD set: It's called Star Trek, it aired on NBC, Gene Roddenberry had creative control of the thing, Dorothy Fontana was producing it, almost the entire original cast was in it, voicing their roles, most of the writers also wrote for TOS, many of the stories were originally intended for TOS, IT'S STAR TREK'S FOURTH SEASON!
If we can put up with "Spock's Brain" and "The Alternative Factor" in the timeline, I think we can include "The Magicks of Megas-Tu" and "The Counter-Clock Incident".