1) in my experience ive never had any snake become more aggressive because i fed him in his enclosure. ive tried both but at one time i cared for well over 200 animals. kind of hard to pull each one out every time i had to feed them.
2) ive never heard of anyone actually testing the nutritional value of rats or mice. even if that were done there would have to be species specific testing to determine the nutritional requirements for that species of snake. boas eat birds and mammals and lizards in the wild. some snakes will only eat other reptiles. so i would say its not a matter of nutritional value of rats vs mice. its more of a size issue. mice are way to small for an adult boa. ive fed some of mine rabbits and even small pigs.
oh, and by the way, i have a pet rat. Humphrey. i love the little guy but i dont really feel bad for the rats i feed to my snakes. thats one of the things you have to deal with being a snake owner.