You probably long ago forgot this topic, but I've filed it for VersionX 2 which is currently in development and is super duper awesome.
I can definitely see it tieing in with that instead of saving, which, like you said, would cause loads of issues

VersionX could probably do this in a non-obtrusive way too (without a huge "Saving" pop up), and it would distinguish between auto- and regular saves.
Very much like the idea.