Skywards Sword is the most timeline conscious title in the franchise, so much so you could say the plot is written to reinforce the idea of the timeline.
So I think what happens with TotK is that despite it being the least timeline conscious title this side of the millennium, any Skyward Sword references, no matter how small, are ultimately read as hints about the timeline just because that is such a strong part of that title.
When you hear Zelda's Lullaby your mind doesn't go directly to thinking of OoT's connection to Totk, but Fi music during Master Sword cutscenes? Seems like a timeline reference because SS is so charged with it.
So I think what happens with TotK is that despite it being the least timeline conscious title this side of the millennium, any Skyward Sword references, no matter how small, are ultimately read as hints about the timeline just because that is such a strong part of that title.
When you hear Zelda's Lullaby your mind doesn't go directly to thinking of OoT's connection to Totk, but Fi music during Master Sword cutscenes? Seems like a timeline reference because SS is so charged with it.