My son is 11, now, and has always been slender but a good eater. I wouldn't worry so much about eating. If you have a good routine set up, he will adapt. My son eats breakfast, lunch, dinner and two snacks - mid-morning and right after school. I am careful about the amount of juices / juice drinks I allow my children. Even moving your breakfast schedule to 8 am, with your lunch schedule at 11:30 am, may be a more desirable schedule. That way, he can come home and have a light snack and, hours later, it shouldn't interfere with the dinner schedule.
Just don't let your son get in the habit of grazing or eating between meals.
I'm questioning that percentile for weight - it seems very low unless your son is very short, also. If your doctor is concerned about his weight issues, then, you may want to consult with him and get some advise as to how you can help your son gain weight.
Good luck.