I don't think there is any time in a horse's life when it is more important for him to be in a well-fitting saddle than right at the beginning. Lots of people seem to take the view that a horse should be well-along in his development and training and then he needs a good saddle, but I think that is closing the barn door after the horse is already out. I have seen a shocking number of horse of 4-years-old who already have arthritic changes (kissing spines) requiring surgery to correct before they ever really get started. It should never be forgotten that nature did not intend for horses to bear the weight of a rider on their backs, so there is nothing natural about it. In my subjective experience, more mature horses that are stronger on the whole are somewhat less vulnerable than younger horses just starting out. I have seen many examples of Olympic-grade horses who would go around just fine with a lawn chair strapped to their backs, but they are genetic anomalies in terms of strength, fitness, and soundness, or they would never have reached that level to begin with. Most of our more ordinary horses have greater innate vulnerabilities, though that varies substantially from horse to horse.
When I fit horses, what I am primarily doing is, well, damage control, really. I think it is definitely true that some horses are "architecturally" better set up to cope with the shock and force created by a rider's body mass in motion than others, but ultimately I think that your best bet with any horse is to put them in a saddle that is as close as possible to neutral for that back shape. What keeps horses back-sound is being able to use their bodies correctly and comfortably throughout a full range of motion, and any saddle that impedes that is, at best, uncomfortable and distracting. At worst, it probably lessens the chances of that horse developing the right musculature and way of going that will enhance long-term soundness and performance.
In general terms, I think that the best thing you can do for a young horse is to be sure he doesn't start out his ridden life with bad experiences of any sort. An ill-fitting saddle can be a bad experience, but honestly, the best-fitting saddle is, at best, neutral. Good saddle fit is something that happens in motion, which is why the "rules" people rely on to assess saddle fit are not very useful and can be downright wrong in some instances. (Hint: It doesn't help that the most important aspect of the fit, which is the tree that the saddle is built on, is entirely hidden inside. Yet it is the tree that transmits shock all the way through its length. Where, may I ask, does this inconvenient fact show up in the so-called rules of saddle fit?)
So I hope this is food for thought. It's very exciting to have a youngster at this stage! It's been a long time since I started a horse (sigh).