They have actively changed the timeline multiple times, eventually pulling a third timeline out of nothing. I doubt there's ever been serious thought put into series chronology outside of the two books in which the two different timelines were published. Again, I say that if they ever really cared about the timeline, we wouldn't be debating it. We would have known about it with each entry in the series.
There's been a lot to unpack here, and I kept meaning to reply to specific posts now and then, but am only just now getting around to it. So yall get a wall of text instead. Enjoy.
There are obvious connections between the Zelda games written into them to begin with, and to dispute that on any level is just being ignorant at best. However, not all of them get translated well during localization, and sometimes things get left out completely or even changed, so it is understandable to feel like Nintendo doesn't care about how they connect when the connections don't get translated the way they should be. If I remember right, Hylia was mentioned as a Goddess in past games before SS all the way back to ALttP. Also, WW wouldn't exist without OoT. Most games reference events from other games in some form, and if you look back, you can see past games work with stuff from newer games, too. The original Japanese text is your go-to for looking into that sort of thing, assuming you feel like sifting through all of that (I don't, but I have a friend that does, and he often shares).
Connections exist, and fans have been putting them together themselves from the start, which is what the intention should have been. It should have remained up to the fans, and it seems that was BotW's intention to return to that, as well. But then Dark Horse came along and made up their own timeline. They are not affiliated with the Zelda team, and to the best of my knowledge, the Zelda team had no involvement with the development of any of the books whatsoever, outside of slapping an "ok to sell" stamp on them after the fact. They pretty much gave them the art and interviews and let them write the rest. It's pretty clear when the games themselves contradict the books. Do not trust the Dark Horse books as gospel or use anything in them to state a case. They are quite literally licensed fan fiction. Just something neat to read for art and interviews and stuff but not evidence for anything.
Back to the topic at hand, as far as AoC goes and "not dealing with its own Ganon", I don't believe that's true. In Chapter 5 when the Calamity begins, that is not the future Ganon swirling around Hyrule Castle, that is this timeline's Ganon. We know this because the shard of malice from the future inside the other eggbot exists separately from it. It's safe to assume they fused into one during the final mission when Calamity Ganon takes on a new form after absorbing Astor, though it's not explicitly shown or stated to be the case. But the fact is their own timeline's Ganon revived, and is gone at the end of the game, so, you know... Put two and two together. (of course, this says nothing about the ganon that's hiding in the basement, but we don't know enough about that one until we get botw 2 to make any guesses there.)
As far as what making AoC canon would do for BotW 2... I think it would be neat if it were used as a side plot in it, not the main plot. Going by the trailers, I don't think AoC will have anything to do with the main plot of BotW 2. Realistically, I think it will just turn out to be a cool stop along the road between BotW and BotW 2. A side story that fits in neatly between the two games. As for what referencing it in 2 will bring to the table... I dunno. I just think it'd be neat, but it might not add anything significant, either. But just because it won't doesn't mean it still can't be neat. At the very least, seeing the present day Champions bring the character development they earned in AoC into their roles in BotW 2 would make me pretty happy. I would enjoy that a lot. But yeah, what they could do with that plotwise... Dunno.
I don’t really get the whole spin-offs shouldn’t be canon thing. Each of the Four Swords games are canon and they are not quite traditional, so why not AoC? If the utterly absurd downfall nonsense is allowed, I think it’s only fair to be able to use this game as another branch for Nintendo to use later on as an excuse when the lore contradicts itself. For what it’s worth I think they just wrote themselves into a corner with designing gameplay first while trying to placate the more rabid fans who wanted everything to be intricately connected, so the timeline book was hastily made up with plot holes and all and then BotW to just fix everything up nice and neat for a soft reboot.
Im confused as to why people think its a non canon spinoff because of the outcome of the game.
If that's the case, then youd have to use the same logic for any other game, right? So then that must mean the downfall timeline also doesnt count. All those game, including a link to the past, are now non canon spinoffs lmao. In fact, might as well say Ocarina of Time doesnt count because the downfall timeline wouldnt exist without OoT...
Also, in the announcement they even stated it takes place 100 years before BOTW..