If some wheels contain symlinks and are incompatible, and some don’t contain symlinks and are compatible, then we should put Wheel-Version: 2.0 in the ones that contain symlinks and Wheel-Version: 1.0 in the ones that don’t contain symlinks.
I can’t think of any situation where a minor version increase + warning is actually useful. IMO that’s just a vestigial feature of the format – harmless but useless.