It is almost certain that any chain pet store you get rats from will source them from a mill... With smaller non-chain stores, it depends on whether they breed their own or buy from local breeders... You would have to ask the store to know.
Life in the store depends on the care the actual workers give and the standards set by management. I have seen some horrible care / husbandry / advice given at petsmart and petco before (mainly fish-related... and petsmart DOES sell feeder fish...), but I have also seen quality care and advice at both stores, again, it goes back to the individual employees. In all the cases where I've seen excellent care, it was due to an employee that went above and beyond, the only case that I know of where excellent care was due to management was when my third cousin was a manager at petco (he sold reptiles on the side), so he made sure their reptile section was top notch and gave out good advice. When he left, things went down-hill. The other scenerios I can give you are of a petsmart employee that kept reptiles as pets herself, so gave out good reptile advice, a petco employee that kept tropical reef tanks, so was excellent with fish, and an animal care manager (or dept. head? can't remember the term she used), who went above and beyond with the rats... she handled them, was the only one that noticed when they accidentally shipped females with the males, etc.
With independent stores, it is hit or miss. I have been in only 2 truly excellent stores (both were mainly aquatics) and one of those is now closed... I have been in some truly horrid stores too.. One that bred it's own feeders... The animals on display looked horrible and the smell was awful, so I don't even want to imagine what their rat racks in the back must have been like.
IMO, unless you are buying from an independent good store that breeds their own or buys from local breeders, it is usually better to source your rats from a breeder, rescue, or even a feeder breeder (if they keep their animals well, etc.). I have nothing against those that buy from pet stores, that is how I got my start, and sometimes you have no other options. But I do think you run better odds of a healthy rat when you get one from an independent breeder (assuming they are breeding for health and temperament).