Reverse shod isn't going to help long term. Sometimes it makes the horse less painful, but causes more damage.
If your horse is doing well barefoot, I'd highly recommend a hoof boot, and put pads in them for riding. Not the same as plastic shoeing pads, but foam inserts like you put in your own shoes. They really help with sole discomfort.
Sometimes they CAN have bone changes that don't cause lameness once the hoof balance is fixed, and that could be what you saw on the x-ray, is old damage to the bone that will never go away,from when you said his feet were contracted and oval with the shoes. Usually, the navicular bone causes pain in motion as the tendon rubs over it, not from hoof testers on the sole. Could be he just doesn't have super thick sole or even could have a bruise, coincidentally. It doesn't make sense that he would be moving sound if the bone damage is really causing an issue. I would get a 2nd opinion, if you can afford it, and stick to your guns about barefoot, I see severe cases of diagnosed nav. disease turn around and regain most/all of their usefullness once the foot is balanced and the horse can use the back of his foot. The internal damage, as I said, never goes away, but they can be comfortable. Whereas with shoeing techniques that treat symptoms, almost always contribute to the deterioration of the bone and tendon, and ultimately shorten the horse's work life.