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Well, I mean Capcom made two games, which were directly based on LA's engine. And that was probably most of the draw for them to reference that title specifically in it's story/characters. Not so much the story the franchise was creating as a whole. To be fair though, you have the very opening the game and Ganon himself serving as potential connections to AlttP. (unified triforce and Ganon being specifically dead by that point.) As well as the shot of the boat after the credits. Which at the time I can't see anyone thinking of anything else but Link's Awakening. Those are the things people have pointed out and it's very clearcut in my opinion.
I don't believe anything needs to be thrown out for them to work either. because again, fairly loose story threads. Save for Zelda's amnesia. ;)