The difference is completely artificial and designed to make pet store owners money.
Almost without exception, most rats sold in the above mentioned pet stores come from mass breeding rat mills. They breed for looks or quantity, and only for money. Temperament is not bred for, nor is health. Even with the best and most ethical of mill breeders, there will be problems. Their stock is not socialized or kept in healthy, low stress conditions. Nor is there any quarantine to prevent spread of illness between rats. Their females are over bred, and often bred too young to produce healthy, socialized rats.
When they create a few litters of rats, they look them over, separate the prettier ones into one cage and the plain looking ones in another cage. This may occur with the mill breeder, or it may occur in the pet store once the rats have been shipped to them. The prettier ones are sold for a higher price and kept in cleaner cages in view of the public. The plainer rats, often from the same litter as the pretty/flashy colored ones, are thrown into a bin and sold cheaply as snake food.
Because of the high stress and overcrowded conditions, the feeder rats tend to be more terrified, and traumatized-the stress of which means they are open to illness- and may be dirtier or suffer more injuries.
However, pretty rats sold as pets may suffer just as much stress which also leads to sickness. They have certainly been exposed to the same sicknesses as the so called feeder rats.
They may label the pet sale 'pretty' rats as 'fancy'. This is misleading. The name fancy has nothing to do with how special one rat is over another. All domesticated rats be they feeder rats or pet rats are Fancy Rats. The word fancy refers to the fact that domesticated rats were bred for Rat Fanciers, or rats of the Rat Fancy.
Ethical hobby breeders will breed for health and temperament first, and looks next. They will produce few litters and track the health and temperament history of all of their rats. They will socialize their babies from birth. They will never sell their babies to pet stores, or to reptile owners. With ethical breeders, there will never be a difference in price between a 'pretty' rat and a 'plain' rat, as they both make good pets.
So, in a nut shell, if you take the time to test the temperament before you buy, and look for healthy looking rats, it doesn't matter if you pay 15.00 for a fancy dumbo, or 2.00 for a feeder rat. They are generally from the genetic line, and with work and patience will offer a similar pet experiences.
Better yet, look for ethical hobby breeders (not back yard breeders) who will support you throughout your entire pet ownership experience and stand by their babies. Best yet, look for opportunities to adopt pets through places like pet finder, or rat rescues if it's possible (not always possible) since they don't put money in the pockets of mill breeders or the pet stores who support them. :)