Simply from a story-telling standpoint, it would be tough to cut in the scenes of the "missing" Black Pirate author, the painter, and the movie special effects artists on Ozymandias' island. It would be a huge WTF for the audience.
But Snyder wants to include all of this in his inevitable director's cut.
I don't think so. He was going to include the Tales From The Black Freighter sequences. The backstory & hints surrounding Ozymandias' plan to create the alien are handled separately from that. Much of the information is conveyed in the "bonus material" that follows the conclusion of each issue.
And Damo, I think you're right. The critique and commentary on the comic-book medium (which escapes me utterly because outside of The Watchmen, I haven't read a comic in 20 years) will likely be lost in the film version. However, I think the book's commentary on the superhero genre in general can still translate to the big screen. And if that is handled properly, I think it can still be viewed as a successful adaptation. I like Moore's deconstruction of the superhero character throughout The Watchmen, and I'm not a comic book reader. I would think that many movie-goers will enjoy that as well.