It matters, but ultimately only from a global perspective. Zelda games have always been designed to be pretty much self contained so that anyone can pick up and play without needing to know the stories of a dozen other games as well. Maybe knowing how the game connects to its immediate prequel is helpful as in TP or WW, but not 100% necessary.
In BotW's case, the backstory so far seems that it is not the story of a Link or game that we've seen before, but someone brand new. This game will likely be self contained, so could hypothetically fit almost everywhere in the timeline where Ganon has had a history with the Hyrule Royal Family. So after TP, or near the end of the decline timeline could work.
I am extremely doubtful of the Adult Timeline though; the Koroks by themselves are evidence of nothing, the flood needs not be the only thing that caused the Kokiri to change form, and if Nintendo wants to use them in another timeline they are perfectly free to. And the Adult timeline is so far split from the Hyrule of the past, I can only see Nintendo using that timeline in non-Hyrule or New Hyrule adventures going forward.
Aonuma said we will discover where this game takes place as we play, but ultimately where it ends up going won't make too much difference, I think. The story is being made to stand on its own, as Nintendo nearly always does.