About 2 years ago my then 6 year old son was shooting his sisters 223 handi with me assisting behind him. I didn't notice as he laid his cheek on the stock that he was looking through the scope with his left eye instead of his right and put it too close to the scope. poor guy popped himself right in the eye with the recoil. Had me crying right along with him. I have to watch him to this day, if he shoots right handed he uses his left eye and uses his right eye to shoot left handed. But he can hit!! He now shoots 44 specials in his 44 mag handi with open sights.
Also, we always use ear muffs when we go target shooting.
Troy, please forgive me for offering unsolicited advice, but I have had experience with youngsters shooting left master eye when they are right handed, and vice versa. Not my own kids, but I used to teach beginners at a shooting club. There were a some who had the left/right thing going on, and were brought to the classes because they were about to give up shooting completely because of it. Their dads brought them to the club hoping the kids might benefit from some outside the family instruction.
It sounds like you are fortunate and your son won't likely stop shooting, but I think it is still worth the effort to coach him into matching his shooting side to his same side eye if at all possible. It is totally your business, but I'd be concerned that as he grows up he'll develop and strengthen his compensating habits and at some point it will be something he wants to change and it will be very difficult. (Consider that he may want to go into the military or law-enforcement, and he will have to be trained vigorously out of any "bad" habits they decide he has.)
In any case it is relatively easy to train at this age, and it's not even too hard for adults - I've coached middle aged folk (women mostly) who were mismatched as to master eye and handedness, and it is 'way easier to teach someone to shoot left-handed if they have a master left eye and are right handed, than it is to break the habit that kind of person developed without coaching) and though he may resist at first, it will be something he'll likely get used to very quickly. In fact I have a friend now who picked up (right handed) one of my air rifles the other day and sighted it with her left eye. When I pointed it out she was quite surprised, she had been shooting that way for years, and hadn't noticed. When I suggested she try a couple of shots shooting left-handed she was reluctant but willing. After doing about 5 very reasonable shots she said she had never really realized all those years of shooting what exactly it was that didn't feel right, but something didn't. And even thought she had always shot reasonably well she decided right then to start shooting left-handed simply because it just "felt right".
Again, no offense intended by this, just that I was so glad to be able to help those kids and ladies a few years back when they were shooting awkwardly, and I figure we need all the young shooters, hunters and tinkers we can get, and I'll do as much as I can to help them enjoy this sport.
Cheers
Kerry