The games we are playing aren't retellings of the same story though. There are numerous sequels for one. Second the concept of a timeline isn't just in Hyrule Historia, it's referenced in the games themselves; for example the hero of time in Twilight Princess and Breath of the Wild.

It's loose, but it's there. These are separate stories, retold many times or not, and the cyclic nature of the battle for the triforce is established game lore.

I believe it's also misleading to say Nintendo doesn't care about the timeline stuff. They care but also make a conscious decision to keep it light and not overly bound or caught up in it.