Nintendo's approach to the lore has always addmittedly been loose.

Things such as the placement of Four Swords Adventures I think are evidence of that. FSA was clearly written as a direct sequel to Four Swords, with references that would put it pre-ALttP, yet their decision to involve Ganondorf basically forced their hand when it came to its timeline placement. Still, while not pretty, the placement of FSA in the child timeline makes enough sense, as it doesn't reject the lore of the world of Hyrule completely.

TOTK ON THE OTHER HAND...

Totk seems to have gone out of its way to throw out the timeline. Yeah yeah, it's a refounding yada yada, but that doesn't change the fact that they still are making the active choice to reboot the history of this Hyrule.

I have heard that totk's story wasn't written by Nintendo however, and was outsourced to Qualia Writers Inc. Feel free to check me on that, I'm not sure. But what I personally think might've happened was that Nintendo set out with botw scraps and concepts, and then actually forgot about the holes that would be left in the game they promised in the 2019 teaser.

The Barbarian set was almost certainly meant to be connected to the Zonai somehow, as was the hand seen in the 2019 trailer. However I think by that point they realized 'oh wait, we can't just throw in a bunch of concepts, we need an actual story here.' Based on the 2019 trailer and their statements from around that time, I think they had the following ideas:

1: Ganondorf was going to come back

2: The Zonai would somehow be involved

3: Zelda was going to fall, to sort of parallel Skyward Sword

4: We were going to get some answers around Hyrule's history.

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And I think this is where Nintendo realized they goofed. The scraps they wanted would wind up causing issues in regards to the timeline because of the way each one is left. A resurrection of Ganondorf would mean confirming which timeline botw is in, which they wanted to avoid doing, perhaps understandably so.

Furthermore, the Skyward Sword reference in the form of Zelda falling (which, if the noises of Fi in the sword are any indication, was deliberate) wouldn't work either because that would require an appearence of Ganondorf prior to Minish Cap and by extension Ocarina of Time which they don't want to do. If there's one thing Nintendo seems stubborn about it's that oot is Ganondorf's origin story, otherwise FSA wouldn't be where it is.

Thus, they panicked and outsources the story to Qualia Writers Inc, a company that doesn't seem to have worked on botw from what I can tell. Qualia reinterpreted the Zonai, and added the secret stones, a concept that almost certainly didn't exist in 2019 (can't see the stone on either Rauru or Ganondorf's hand). I'd even go so far as to say this reinterpretation is what caused the delay, just based on when the trailers were being released.

Noticeably, the trailer from February 2022 doesn't feature any Secret Stones, though it does have the newer Zonai arcitecture.

TLDR: Look, I don't have much of an official basis for this, but based on what I'm looking at, it seems the original version of totk had to be changed when Nintendo realized their story contradicted the lore too much, so they outsourced it to a new company and hoped the gameplay would be enough to recreate what botw started.