A little late to the comment party, but I'm certain the TRT will happily work with the authors to get this solved in a way that won't affect any existing users sites.

The first thought that comes to mind is ensuring backwards compatibility by only displaying the content relating to grey areas to existing users on update, and hide it for new users altogether.

I agree with the TRTs approach though, that themes should deal with visual aspects, and the easiest way to identify this is by asking your self "if I change my theme will I lose this content" (that's not to say I agree that adding plugins can be difficult for the end user if you need a handful of them for basic theme functionality, but at that point I'd wonder if the theme isn't overly complicated to begin with?).