In the "Hero Defeated" timeline, there was a war called the "Sealing War" and it was also when Hyrule was declining. In that war, since Link was defeated during the events in OoT, the sages had to seal Ganon however they can to stop him from growing in power. Which leads up to "A Link to the Past".
But there's also another thing that shows BotW isn't in the "Hero Defeated" timeline. In the Child timeline, Ganon had a physical body. However, in BotW, Ganon was just made up of malice and he was trying to reincarnate himself into one of the Giant Ancient weapon bodies (The Ganon Blights) that was mentioned in Zelda's diary in her studies when she tried to find them beneath Hyrule Castle, but couldn't. Anyway, since Ganon was trying to reincarnate himself with an actual body, it means that he never had a physical body in the events coming up to BotW. Which is why I think that after Ganondorf was killed at the end of TP, his malice appeared in Hyrule at some point and was sealed by a different Link and Zelda in a different point in time which was 10,000 years before BotW. Luckily, they were prepared as the people (most likely the Sheikah) created the Guardians and Divine Beasts, controlled by the four Champions, to aid the princess and the hero into defeating and sealing Ganon.
Well, that's what I think, because there aren't any games that show a trace of any of the Guardians and while Skyward Sword does have similarities of that "technology" in those ancient robots, they weren't built by the Sheikah and they existed way before Skyward Sword when the Sheikah haven't came to be, yet. So I think BotW is set very far into the future of the Child timeline.