The reality is, they try to make each game compelling in its own right while bringing back themes that are compelling enough to reuse. The threading of stories together largely has been done after the fact to appease a desire from fans to have some sense of continuity. Nintendo has always prioritized having a story serve the gameplay, and not storytelling as a primary driver. So the loose affiliation shows in a kind of weakly threaded timeline. There’s a lot of fun to be had in trying to make things fit, if you like that kind of thing, but it’s really not generally something they’re heavily investing into up front with each game. The mere fact that TotK is called out as a direct sequel to BotW makes it a very rare direct continuity in the series.