I agree that they MUST be on the same timeline, but I don't think 'the split timeline wan't even developed' yet is a good argument cause it was post
OoT and I think they had the split in mind already to explain the old games.
There are some plot lines that seem to be 'completed' one way round, and others the other, I think it's entirely open to the player.
The official site puts Seasons first and historically the first game in an arc has a Red logo and later ones change, but I prefer
OoA first because I prefer it, it means you can have the hyper slingshot to make Twinrova easier and I like the alphabetic-ness of A before S.
But I think S just about makes more sense with publicity media and stuff.