JuicieJ
SHOW ME YA MOVES!
I would love for it to be an alternate legend, to be honest. But it seals a really gaping hole in the timeline by bringing a new Ganon into play - the ostensible death of Ganon at the end of Twilight Princess, yet his reemergence trapped in the Sacred Realm in A Link to the Past. Thus I find it hard to place it outside of the current timeline with the games we currently have available. If it is an alternate legend (which would be really cool, a nice fusion of a timeline and literal legend theory), there is plenty of room for a full game between TP and ALttP, but we don't have that yet. So I place FS/FSA in the hole to put a tenuous, not perfect, but solid, seal on that hole.
What's ironic about this is that FSA was originally planned to be the Seal War (as they scrapped OoT being it, hence WW taking ALttP's place being a sequel to the adult ending), but was decided not to be about halfway through development. Anyway, yes, there is a gap, but it can't be filled without contradiction as of yet, as you mentioned (and I'm glad you see that). This gap is the reason I want Nintendo to make a game that goes in-between TP and ALttP that brings about the Seal War.