And there's no reason it couldn't have happened. Filmation did two different Batman cartoons, one in '67 and one a decade later. And in the late '70s/early '80s they did new animated versions of their live-action characters Isis and Captain Marvel. Not to mention that they revived Fat Albert once or twice after years of reruns, and did Gilligan's Planet as a sequel to The New Adventures of Gilligan.
Around the time in question, Filmation was doing the fantasy series Flash Gordon and Blackstar (sort of a prototype for He-Man) as well as animated versions of The Lone Ranger and Zorro. A new Star Trek could've fit in reasonably well.
Agree, Filmation missed out on this. It would have been a brilliant TMP
era animated series to fill in what happened before WOK