Dental malocclusion can still happen in young rabbits, though acquired dental disease is more likely in older rabbits. So a congenital dental problem is still possible.
I would still want to get a second opinion from a more experienced rabbit vet. I wouldn't have much confidence in a vet that says there isn't much else that can be done, when a follow up exam and no xrays or blood work has been done. In the least the vet can give an opiate pain medication to help control the pain and alleviate the poor bunnies suffering.