Spine currently allows animations (and skins and events) with the same name, but different folders. If a user does that (I understand you don't), then if we had a setting to export without the folders in the names, then they'd end up with duplicate names and that would break things.
Ideally you would just use the folder names as part of the animation name. Even WalkAnimFwd/WalkFwd_Start
isn't really a problem. Is your issue that you've been using WalkFwd_Start
in the code since before Spine had folders? I'd think it should not be a big problem to change the names you use at runtime.