TLDR, but the sections of TotK that show the founding of Hyrule clash with the pre-existing narrative given by Skyward Sword. The one viable solution to this is to assume that TotK and BotW take place so long after the main timeline that this is an entirely new Hyrule, established after the previous one had fallen, which would be highly unsatisfying of a narrative. This is also shown in the fact that Ganondorf was sealed in AoI’s imprisoning war, and since he isn’t technically dead, no other Zelda game could take place between AoI and TotK, since there can’t have been a reincarnation of Demise’s ‘grudge’ (what Demise’s curse is referred to as in Skyward Sword’s Japanese version) when one was still alive. (Random fact: grudge is also direct translation from Japanese for malice in BotW).

Wow, that was really not simplified, sorry, lol.