No, both plots will need to be developed throughout the movie. You cant just have Ozy bring it up out of nowhere. For the squid to not seem out of place, you need to have the scientists and artists go missing. You need to have The Black Freighter, so people know who Max Shea is, you need the scenes of the people on the island, and then leaving the island, and the boat exploding.
With the new plot, you have that machine that Jon is working on when Rorschach first visits him. Then there' the project him and Adrian are discussing while Jon's multiples are in the other room freaking Laurie out. Also apparently there's a little bit about it when the two meet at Blake's funeral.
Notice how in one case, all that has to happen in extra scenes, purely for the development of this plot, whereas in the other case, it happens in scenes that would exist otherwise, and take the place of otherwise useless stuff, like Jon looking for gluinos or whatever.