So we all know GTD is about gaining Control and Perspective, in equal measure if possible. Perhaps then the trick is not to fiddle with the Control lever to try and accommodate some large projects but rather the Perspective one? Instead of stressing and complicating about how to identify and manage sub-Projects why not bump up a significant project (in the non-GTD sense) to the 20000ft Horizon and make it an Area of Focus? That way you can happily have all the GTD Projects you like at the 10000ft level that flow from that?
Just a thought.