This is true, Nintendo have placed a 'universal outcome' shift at the point of Link defeating/being defeated by Gonnondorf in OoT, there's no reason to say that there couldn't have been another alternate universal timeline before SS, maybe an alternate universal timeline that took place before SS and depended upon the Heroes outcome prior to the shift in OoT?
Heck there could be more universes undiscovered still, the goddesses after all are omnipotent beings and don't have to be restricted to one contingency.
Well, I don't think Nintendo would go so far as to start a new "timeline proceeding Skyward Sword," but I think there exists the possibility of another story (or two) which predate
In retrospect, I think I see where Nintendo was coming from when they said creating a definite beginning, and a solid timeline sets limits. I'm not saying it's entirely impossible, but with what's given in SS seems to set limits on a story proceeding it. And if such a story ever comes into fruition, Nintendo has to do it JUST RIGHT, or the fans will rage.