Haha yes-- in this case for BoTW to be at the beginning of the timeline, the Rito wouldn't exist yet, as they are only present in Wind Waker and beyond, not that it's impossible for both to exist.
The Rito are fundamentally different though, right? WW Rito are humans with bird beaks, but BotW/TotK Rito are actual birds in humanoid stature. Personally I always assumed they were Loftwings that became sentient.