I feel like that should be the case, but Nintendo has put themselves in the corner by releasing an “official” timeline. But this would have been pretty easy to fix by simply not calling Rauru the first king of Hyrule. And not making him Zonai. If he’d been a Hylian king that wasn’t the first it would make perfect sense…
BotW didn’t fit in any one timeline. It had components from all the timelines. However, they said it occurred at the end of all 3 timelines. So my headcannon was that there was a large merging event that combined the timelines back to 1. And I expected it to be a “reset” where games would only reference the story from that point forward to kind of “clean up” the past lore without dealing with it. That clearly didn’t happen since TotK was all about history