I read your post before you edited it and I beg to differ on some of it. I have been raising and breeding rats for over 10 years now, not as feeders, but pets.
You might have issues with feeder breeder males fighting with each other, but well socialized males will never have a serious fight. Keeping rats in a harem style group is VERY stressful to the females.
As far as letting a pair of females raise their young together, 99% of the breeders do it and it works perfectly. I personally let my females raise their young individually (or two weeks apart). I just had a female drop 28 young and another 17. I didn't lose one. Out of all of the years I've been raising rats, I've lost less than ten young. Most due to a mother abandoning her young. Which might I add, hasn't happened since spacing the litters two weeks apart.
Genetic wise, I said "one he liked". Meaning that color, dumbos, coats, etc do not produce more young. It's often said that albinos produce more, but I've noticed I get larger litters from my self rats. I also wouldn't imagine him going to the pet store picking out the most aggressive male they had. Yes, certain rats carry genetic dispositions. That being said, I've raised some of the sweetest babies from rats that were aggressive.
To each their own.