I'm not sure why there is a distinction between Live action and animated. Continuity isn't based on that. All the TV shows and movies are looked upon equally. (Depending on the current IP holder/franchise runner)
I think the issue with that started with the whole TAS debacle (Is it canon? Is it not canon? Are only parts of it canon, or is it all canon? Etc etc.) Not to mention that TAS was always looked upon, even by its creator, as a cartoon for kids. So for the longest time the idea of animated Trek being taken seriously was up in the air.
Then the first Trek animated series in 47 years comes along, and it’s a comedy that rarely takes itself seriously. Then a second animated series that was ostensibly made for kids, turns out to have been too cerebral for them, and was not taken seriously as a kid’s show (despite it turning out to be the best Trek show CBS produced, IMHO.) And then to add insult to injury, CBS’s ‘tribute’ to TAS was some of the most horrid Trek on TV.
So no, I wouldn’t say that animated Trek has ever been looked upon as equal to live-action.