Nintendo

Majora's Mask picked up with the Hero of Time after he returned from the adult timeline, it clearly shows that it's the same character. Then Wind Waker's opening scene showed the same Hero of Time beat Ganon then disappear and then Ganon comes back ; the king of red lion also says he was hoping the Hero of Time would return, but that never happened, and instead he found the new hero of wind. And then Twilight Princess shows Ganondorf was arrested for trying to betray Hyrule before he could execute his plans, but then he still got the Triforce of Power ; and the Hero's Shade is confirmed to be the Hero of Time whose achievements were not remembered (because he erased them by going back in time) and he couldn't pass on his skills. It's hard to pretend that those games are not connected when it's right there in the opening and the cinematics and it even uses the same name (hero of time). WW and TP ignored each other, but that's because they were the different timelines.

The timeline split wasn't invented years later to fix that. The OoT timeline split was explained by Aonuma immediately between Wind Waker and Twilight Princess, precisely because people were wondering if the two games contradicted each other - Aonuma is the one who pointed out that returning to the past created a second timeline, and he explained that right when they released Twilight Princess. It was all right there in the games as they were coming out, Hyrule Historia simply confirmed it years later for the release of Skyward Sword, that wasn't made up by fans. The only thing that Hyrule Historia did that the fans didn't expect was the third split, with the fallen timeline. That one still doesn't have any coherent explanation, that's the part that Nintendo is probably trying to ignore, that the fans don't like, and that makes some people think it's made up nonsense.

BotW was a breaking point where they decided to do something different and not use the timeline and put it in the far future, but the Rito and Zora are not a contradiction, all it needs is the confirmation that the Rito already existed before the Zora turned into them. And that happens in Twilight Princess HD, the remake where they added a texture for Hyrule Castle with a relief showing a Rito. So the Rito did exist even in the TP timeline. TotK doesn't contradict Ocarina of Time, it's not the same event, it's a different Ganondorf - we already knew there was more than one guy called Ganondorf (it's a different one in Four Swords Adventure). There's a gap of about 300 years between the events of TotK's past and OoT.

If you want a fan theory, I think TotK and the Ouroboros symbol it uses as its logo shows that this Zelda is the one who creates her own timeline by going back to the past. She creates the split 300 years before Ocarina of Time, and that leads to the fallen timeline, at the end of which BotW happens. Without her, things play out differently and result in other events that end up in a civil war and into OoT centuries later, but with her, Ganondorf is sealed and the events play out as described in Link to the Past, which are slightly different from OoT. It resolves the fallen timeline and the fact that OoT was intended to be the war described in LttP, but it ended up playing out differently, and they never explained that other than "uh, Link died in that version" in Hyrule Historia.