But our boys, especially the older one, campus cafeteria will most likely be off limits due to his food allergies. Unless he'd want to snack on lettuce like a rabbit in which case there's still a chance of cross contamination!

At least in our kids case the food allergy issue is another big reason why off campus housing would make more sense.
I don't know how complex/fatal his allergies are but many school cafeteria's are VERY aware of different allergy/diet requirements. Not all school cafeteria's are created equal, some do this better than others. Your son probably would be best preparing his own food, but some dorms provide special kitchens for these highly allergic kids. I wouldn't just discount school cafeterias by how they were in the past.
But as to your comment that it would save to put both boys together in apartment. You are right it might, but that depends on a lot of things aligning such as both boys wanting to attend the same university & apartment. As most students who live in apartments share anyway, I'm not sure how much it would really save.