JSON Feed is in a catch-22. Not many websites use it (and none can use it exclusively) because not as many clients support it. Few clients support it because not many websites use it. While an auto-discovery spec would be great, having multiple feeds is currently the only way to add JSON Feed and break the cycle.
> What we really need is an update to the auto-discovery spec that says "these two feeds have the exact same content, if you support both formats only show your preferred format to the user"
You could do that right now by having 1 URL that changes what type it returns based on the request's "Accept" type. However, I don't know if any websites/clients actually do that, or if it would break older clients.