Similar to what I said in my previous post...
At first, that seems like a great idea. I like the concept of "story matters." However, for me (and I assume at least some other players of rpgs,) mechanics can also be part of the story. I think that some rpgs are better suited to certain types of stories due to their mechanical choices; with the very different approaches even within the D&D brand, I'd say that even different editions of D&D cater to different styles. There certainly are ways to modify a story so that it fits better into a game, but, in the end, I still believe there are some styles of story which are generally counter-intuitive when placed side-by-side with some mechanical choices.
I'm not suggesting that the approach can't work. It's simply my believe that not all stories/adventures fit equally well into all editions of the game; I think ignoring that is the wrong thing to do. Instead, I think embracing that would allow different elements (editions) of the brand to be highlighted by showcasing their strengths rather than trying to pretend every edition handles the same stories equally well. I suppose what I'm trying to say is this: "ze game" does not always remain "ze same." In many cases the differences may not be noticeable, but I believe there are enough cases in which the differences are noticed that it's relevant to consider mechanics when speaking about story.
I think your suggestion of notes and things of that nature would greatly help, but I also believe there are times when a story may be so at odds with a particular edition's mechanical choices that -even with notes- the results may not be as good as they otherwise would be with a different edition... or even maybe a different rpg.