A horse at a barn I used to board at fractured his withers - I don’t know all the details about the injury or rehab, but if I recall correctly, he was back under saddle and jumping in about a year. He seemed comfortable at first, but started refusing and was brought back out of work due to SI issues. I have no idea if the SI problem was the result of an injury that co-occurred with the wither fracture, or was compensatory, or totally unrelated. That’s about when I changed barns, so I don’t know the end of the story.
He definitely had misshapen withers due to the injury, but I think not in a location that interfered with the saddle (in an obvious way, at least). I imagine the ability to fit a saddle comfortably with this kind of injury is extremely variable.
Maybe try sizing up the tree width to make room for padding that can be trimmed to fit his/her shape? That might give you more flexibility in fitting the whole back if a wide channel under the cantle isn’t needed, for example.