I'd even say Majora's Mask made things a bit rocky, b/c prior the timeline was simply OoT>LttP>LA>LoZ>AoL, and like you mentioned OoT was showing certain backstory elements for Past, but then we get MM where it shows us Young Link after having gone back in time from the future he left behind, so....did the split already happen? B/c if the events were undone then LttP couldn't follow up MM unless I'm missing something. And of course Wind Waker added it's own continuity, so the question was always where did the 2d games fit? Especially at this time where it feels like they were in some weird limbo on their own since they couldn't follow up either MM or WW