I'm of the opinion that Sephiroth does diminish Sora's chances a little. After all, KH and FF have such close ties and everything.
That said, FP2 is nigh-impossible to predict at this point. ARMS didn't seem like it had much of a chance once base roster was finalized. Steve seemed like a longshot after Banjo. And now, pretty much no one was expecting Sephiroth. Meanwhile, Travis looked like he had stellar chances, and he got costume'd. It truly feels hard to try and guess what's coming, though I'd say Sora still has good chances overall. It helps that he's also pretty popular in the Smash speculation scene and very popular with the general gaming audience. This is, of course, with the hopes that the "too expensive" rumor is false, and the hopes that Sora doesn't get costume'd in a week (feels like that would be very unlikely to happen).