You know I am very positive about using Cornerstone in all my projects, but the difficulty I am having is that the starting point is not real-world ~ nobody, or so it seems ~ does the loop quite like WordPress says they should.
May I make a suggestion?
While I can understand why you don't want to end up supporting the whole WordPress community in whatever theme they might want to use Cornerstone, could you at least give us some "real-world" integration examples to get us started?
Like Genesis for example, or Thesis, Page Lines, Catalyst, Headway and maybe one or two others like Thematic or Gantry.
Just a primary list of example code snippet examples to show how it could be done?