Notch has said they phase, but that video looks very much like destruct rather than phase through the blocks like a ghost.
Originally Posted by http://www.reddit.com/r/Minecraft/comments/l9m8m/why_ender_dragons_wont_spawn_in_main_world/c2qx6qk
Originally, it hit walls and couldn't move through them. It awkwardly turned around and changed direction. The player can easily create walls on their own, and trying to make an AI to properly navigate arbitrary terrain before the code freeze next tuesday isn't feasible when there's so much more we need to do.
And since the dragon is going to start out as an overpowered boss enemy (I'm definitely adding less overpowered dragons for the main world after release), we don't want too many easy ways to deal with it, so we had a short design meeting and decided to make it cheat.
Originally Posted by http://www.reddit.com/r/Minecraft/comments/l9m8m/why_ender_dragons_wont_spawn_in_main_world/c2qxhwh
They will be different dragons. The Enderdragon will probably become larger, and the ones in the main world will be this size, won't go through terrain, and will be red because dragons are red.
Hopefully the snowman issue will be fixed as of tonight when we restart the world (Pre-release 4 of Beta 1.9 is out