The leadership opportunities as a freshman at a prep school are not what West Point is looking for in terms of their application - they are not going to be student body president or team captain of a sport, etc. The second year at these schools usually is the final year before commissioning in the reserves. Basically, if you don't get in that first year, you face the choice of changing to a different school or commissioning/not going to West Point. The question becomes, is the potential college academic boost going to be enough to overcome a lower leadership score and earn them an appointment. In most cases, why bother with a prep school when you can do the same at a normal college.
You mention late bloomer in that he hasn't done much in the way of JROTC, but only a fraction of cadets did that in high school. What clubs has he led (always opportunities to do that as a senior), has he worked on yearbook or the school newspaper, does he have a job that he puts regular hours into, did he work his way up in scouts, and so on...leadership in extracurricular activities is varied. Having something might not make an individual a standout, but it keeps them in the game. Further that is only a third of the overall leadership evaluation along with the teacher evaluations and athletics. Thinking back to stats, while almost all that gain admission have a varsity letter, only about 60% were a team captain. That means your son stands out more in that dimension of leadership and that helps average out that leadership component.
As far as enlisting, there are many schools and opportunities to shine as a young Soldier that West Point recognizes. Honor Graduate or Commodant's List at schools like AIT, completing airborne, air assault, etc. It may take more than a year at the enlisted route, but it doesn't close doors so fast or cost so much. Further, they come with their own nomination through their company commander. Finally, it is always an option to determine if being an Army officer is the way to go. After a couple years in the Army, your son will know if that is what they really want to do.
Really, the individual to have this discussion with is the RC and the time to do it is in January/February when they can make a good recommendation given the competition in your district, the overall strength of the file, and potential for improvements at the different paths. It may not even be necessary if that BFE is already on the way at that point.