That is a really good question. I would eventually like to have all of my females seperated out once I know for sure that they are going to have a litter. I have had issues with litters being born at diferent times. They do get mixed in with newer litters and I am pretty sure that there is some loss associated with that. I do not believe that I am getting the maximum survival rate that I wish I could have due to that.
I like to pull my 4 week old rats to minimize that, but there are times when as you said, there are litters that are 2-3 weeks apart. The moms do their best, but I am sure that I lose 15% of newer litters because of the fact that they have to compete for food with the other litters or they get trampled/suffocated.