The three numbered titles tell the perspective of Sora in a much larger plot that, especially in KH3, requires the context of the non-numbered titles.
Those "side stories" aren't side stories. They're integral, especially to KH3. There are literal hours of that game that makes zero sense without playing the non-numbered titles.
There's literally not a single part of the MCU analogy that doesn't work. They're different sections of the same story in the same universe about different characters that all coalesce into a single story about the same overarching plot. Outside of the non-canon Verizon game I mentioned, the only title that even comes close to qualifying as a "spin off" is Union X, but the events of KH3 have shown more now than ever that Union X is setting the series up for the next arc.
Because when people think about spin-offs, they think about junk like Raving Rabids, Fable II Pub Games, and Shadow the Hedgehog.
Well that's just not what spinoffs means, dude. Sorry. And side stories can have important plot points that inform your understanding of the main story, that doesn't stop them from being side stories. And no, MCU isn't "different sections of the same story". They're different series. You don't have to watch any of them to understand the Avengers series. You don't have to watch any series within the MCU to understand any other series. That's why the MCU does so well.
Also, you undermine your own point by including Shadow the Hedgehog. It's a spinoff, but it includes story points that intertwine with the story points of SA2. Spinoff also aren't junk. Is that why this upsets you so much? Because you think spinoff inherently means junk? Luigi's Mansion, Metroid Prime, Mario Kart, all the Metroidvania-style Castlevanias, Persona, Mega Man X, Donkey Kong Country, for that matter even Super Mario Bros. (also technically a spinoff of Donkey Kong) were all spinoffs that became their own much beloved game series. I'm not trying to undermine some of my favorite Kingdom Hearts games by calling them spinoffs. I'm just saying I wish the presentation was different, and no, not just with a superficial numbering system.