The timeline being open to change is not the problem, the problem is the recent two games feeling like they're not connected at all. Every other main game from Nintendo, not Capcom, felt connected to a previous game. TP and WW feel and are connected to OOT, PH and ST are connected to WW, ALBW is connected to ALttP, MM is connected to OOT. Are there contradictions and is it overall a mess, yes, but they're still all connected, it still overall feels like a cohesive connected universe. BOTW felt like a soft reboot, TotK feels like a hard reboot.
Plus frankly it's just not fun to discuss a placement when there is no placement. It's not like placing the Oracle games or trying to understand where FSA should go, neither BOTW or TotK fit anywhere, both games are equally incompatible with any timeline, and without a answer any discussion eventually turns into a cyclical back and forth of overanalyzing random inconsequential throwaway lines or items or cameos, till eventually even the most stubborn individuals give up.
Discussing things like the Eight Heroines is fun, and is a testament to the world-building of BOTW, but trying to place it on any branch is fundamentally pointless.
I think you're not describing all Zelda games, but the Aonuma era of storytelling
Aonuma as a director cared a lot more about interconnected story than his predecessor, and his take on it is very different from his successor. Majora's Mask being a direct sequel to OOT might be chalked up to asset reuse and economy of time, but WW, Twilight Princess, Phantom Hourglass, etc all returning to the same well is a mark of how Aonuma preferred to do his storytelling
Fujibayashi's era seems more concerned with legends, grand sweeping tapestries of infinite antiquity, and stories that don't fit cleanly into timelines and play around with what we
thought we knew about the games. The Oracle games, Minish Cap, Spirit Tracks, Skyward Sword, Breath of the Wild, and now Tears of the Kingdom, are all games that are focused more on the mode of treating the Legend of Zelda as a canvas on which to tell legends, which may or may not be precisely true when compared directly to each other
It's also worth noting that we're in a part of Fujibayashi's era where we're revisiting the themes and motifs of the earliest days of Zelda: Breath of the Wild is about the dark beast Ganon returning from a poorly understood banishment and seizing Hyrule, very much echoing the first game, while Tears of the Kingdom is about dealing with the fallout of the Imprisoning War where the Demon King Ganondorf was sealed away by ancient sages in the earliest days of Hyrule, which is basically A Link to the Past all over again
It's perfectly fine to prefer Aonuma's era of storytelling. A lot of people do, and for good reason! But that doesn't mean that you shouldn't, much less
can't, try to engage with Fujibayashi's games. There's plenty to engage with! We're just returning to a much older era of timeline conversations, from back before Aonuma's interconnectedness ruled the day