What reason might a doc prescribe singulair (montelukast) at dosing for >6yo for a smaller than avg. 3y.O.?

Dose per weight. In general pediatric medications are dosed based on a child's weight, this enhances the likelihood that the dose will be safe for a child's metabolism. Singulair (montelukast) dosing recommendations, from the manufacturer, are based on age and your doc may have suggested the higher dose due to size or severity of symptoms.
A few possibilities. Medication doses are guidelines with exceptions. Some kids have more symptoms and benefit from larger doses. Other kids weigh more and need bigger doses. Certain medications lower the effectiveness of other meds, so the other meds need to be given at higher doses. Singulair (montelukast) for little kids is 4mg and for big kids is 5mg (doses are similar), so maybe a doctor feels the difference is not important.