When Matthew Fox agreed to what Kimmel was saying, I think it was only because the ending was left to our interpretation. The scene from the season 6 premiere was shown because Kimmel thought the turbulence meant that THAT was the moment Jack died in the real timeline (lying beside Vincent on the ground with his stab wound). Matthew didn't confirm or deny but said it was very much possible. We may never know. Kimmel's like the rest of us, he has his own theories
I think most people are in agreement that the alternate universe was sort of like a non-denominational heaven.. you could even call it purgatory if you like. An afterlife sounds about right too. It was just a universe that was created to allow all the Losties to meet each other again and be at peace. It never existed in real life though. Jack and Juliet were never married, they never had a son, Sawyer was never a cop, etc.
However, everything that happened on the island DID happen. Locke is dead, Jack dies. Hurley and Ben become #1 & #2 protectors of the island. As for Kate, Claire, Sawyer and the rest of them on the plane? Well, that's open for interpretation too. They could have made it back home, or they could have crashed into the ocean 10 minutes after takeoff. (I personally like to think they made it home so that Kate could look after Ji Yeon, Claire could be reunited with Aaron and Sawyer could find his daughter). The alternate universe was timeless in that it took place after everyone has died. Could have been sooner than later, or could have been 50 years down the line. Just like Christian told Jack at the end: "it could have been before you (aka Boone, Shanon, Sayid, Sun, Jin) or long after you (possibly Desmond, Hurley, Ben, Kate, Claire, Sawyer.. who knows!)" . That's the beauty of it.
I've rambled on but I hope this helps a bit!

It's been a few hours since watching the finale and the more I've allowed it to sink in, the more I've come to accept and be at peace with it