As the mom of infant twins, I can say that the comparisons by others (both adults and children, even total strangers) of the two babies are incessant.
People really do seem uncomfortable until they have some way to distinguish between the two girls, and labels (the "smiley one", the "active one") seem to be a favorite way to do it.
I try to be simply factual about differences and avoid comparing at all costs. L loves looking at faces. E likes faces but loves squeaky toys. These are facts, but at 4 months old does not mean that L is more social or a "happier" baby in comparison to E, and I correct (politely) anyone who tries to label them that way.
I would just be upfront about it with your DSS and explain that he probably doesn't enjoy being compared to others (friends or his classmates), and you don't want him to get in the habit of comparing the babies. Even though they can't understand now, it can be a hard habit to change later. Then you have to disengage the part of your brain that is making the comparison as well. If he comments that his sister is rolling over (and only makes that statement), you need to stop making an internal comparison.
For example, if someone says that L smiles a lot, I say thank you and don't go to a place mentally where I'm thinking "but E smiles a lot too, you're just not seeing it at the moment!"