Maybe they said the flashsideways timeline isn't an alternate timeline because it's the main one. And maybe everything we've seen on the show is just a sojourn from that "main" timeline.
But those are two separate realities from each other - if that's what they mean, they are really being devious!
After this week's ep, I'm getting the strong impression that the flashsideways characters are remembering the other reality on the island because that is their past. There can't be two independent realities with two Sun's and two Jin's and two Sawyers, etc. That wouldn't work dramatically because only one of each character is the "real" one for us. They need to literally be the same people, just at different points in their lives, or else the audience will feel cheated that they're watching a bunch of new characters whose stories we haven't spent years fretting and theorizing over.
Something will happen in the series finale that knocks everything on its head and sinks the island. The whole world forgets about the famous Flight 815, and so do all the characters. They don't remember they were on a Flight 815 before. That also explains why Desmond was on the plane - it's not the same Flight 815.
Dead characters like Charlie and Boone will come back to life. The original Locke also revives, yippe! I dunno about Shannon and Juliet. I guess it depends on what happens in the finale, who gets resurrected and who stays dead. Jack's son suddenly pops into being, and both he and Jack, and Jack's ex-wife remember a past that never actually happened, with the kid being born and growing up. Sun and Jin don't recall being married before. Ji Yeon has sadly blipped out of existence but presumably she's re-blipped into fetal stage. Ditto for Aaron.
The finale has the characters increasingly remembering their former lives and realizing their current reality and memories are all wrong. How that situation is resolved, whoooh, I have no idea, but I'm sure that it happens because Smoky gets off the island and timeline havoc is the result.
This is pretty crazy shit, but I'm going with it as my prediction. It's really the only scenario that I can think of that will work dramatically without feeling like a cheat or that this season has been a waste of time.
The one thing that would upend this theory is: has the year the flashsideways are taking place in ever been established? It "should" be happening in November 2004, right?