Perhaps your vet is using the term rotation to decsribe that he has really upright coffin bones (and sounds like contracted feet), but without actually separating, so he's not truely "rotated" at all. I'm assuming, because descriptions on the internet can be easily misunderstood, but I'm going to go with that.
It sounds like your horse has vey contracted feet, which to answer your question of whether it could lead to lamness down the road; YES, it can. Contracted heels are a sign that he's not landing heel first and utilizing the shock absorbing properties of his foot, and his body is getting the full concusive force when he's working, He's at a higher risk of Navicular syndrome (esp since his coffin bone is tipped downward) and developing arthritis. It may be a genetic predispostion, as in conformation makes it more likely for him to have upright shoulders and move in a way to promote his hooves to be this way, but many times early trimming in foals is skipped and they are kept in stalls to protect them and the foal misses the opportunity to develop the back of the foot properly.
Regardless if it's not bothering him now, the coffin bone should not be considered "okay" as is. There should be some effort to promote heel first landing and correcting the angle to preserve his soundness for the future. It may not need to be anything dramatic, but subtle changes can help. He may have issues higher in his body that also limit his ability to land heel first if he's compensating, so his whole body should be examined and considered when trimming him. It's rare that all four feet would be exactly the same, the fronts and hinds are usually at different angles. Unless he's a mule, but even they must land heel first with the coffin bone landing flat, not on it's tip. Too many toe first landings can actually damage the coffin bone and erode the tip in bad cases. I would get a second opinion from a qualified farrier and maybe have another vet check out thos xray films, personally. Contracted feet can lead to serious lameness, and the coffin bone should never be allowed to stay "rotated" and be acceptable.