While the title is generic, I can only confirm that this is the case for the Glider and its wings. The glider itself is not registered, but the wings are. I would encourage a full review to make sure this is not the case for any other items.

So I do not duplicate the issue. I am running into the same problem. Changing the recipe with crafttweaker isn't working. And the solution with resource packs is not really great either for a public modpack and different servers.

Item can be disabled, sub-items (based on damage) can't. Right now I don't plan to split that item into multiple ones before 1.13 (when it will be mandatory).