Breath of the Wild isn't in any timeline. It's very clearly leaning into the original idea behind the series: that the story of Link, Zelda, and Ganon is a legend that's told over and over again, where the details change slightly every time. The game has its own internal continuity; 10,000 years ago some stuff happened with Link, Zelda, and Ganon. Then 100 years ago some other stuff happened. But that's all internal to this game. The multiple timelines thing from Hyrule Historia is a clumsy and convoluted retrofitting of fandom's obsession with "canonicity" to a series that never really had any intention of adhering to strict timelines. It's The Legend of Zelda, not The Complete and Accurate Historical Account of Zelda.
Furthermore, Zelda is a video game first and uses storytelling to frame the game experience. There's no grand narrative planned for the series. Nintendo makes a game that fits into the series thematically and makes some references to other games to please the fans and then moves on to the next one.