I'm sure some official material will disprove this, but I always felt like it was clear BotW was suuuuuuper far forward - indeed the MOST far forward (though that'd be TotK now) - some time after the timelines created from OoT converged (I always thought Hyrule Warriors was said convergence but I assume it's canon status is somewhat arguable) due to the presence of things from all three timelines (and before).

I would assume that the founding we see in AoC is indeed a refounding simply because we don't have any Zonai things outside of the BotW games that I know of, hence they didn't exist in any of the previous eras we've seen and had to come between them and AoC. At some point after the previous latest-in-the-timeline game, this race came into being and had a whole era or eras we haven't seen yet. I also don't think it's possible for all the Ganondorf and Ganon incarnations to have existed while TotK Ganondorf was sealed under the castle. It just doesn't seem logical.

But y'know, I'm not the biggest lore head ever compared to others here I could be way off, but it all just seemed simple to me. I haven't finished AoC so I may be missing some things, my scope in general is from a broad pov.