A breeder, most likely, takes great pride in the few breeds they specialize in. These chickens are looked after closely and are of better health and conform to the standard more so than birds from a large hatchery whom is merely in business to make money.
I have a few breeds I plan to sell eggs from and raise chicks to sell. Anyone else on here that does the same thing will understand this is DEFINITELY not for the money. I travel hundreds of miles (and spend hundreds in gas

to get the perfect birds. I then blow more loot building them the most lovely accomodations....and so on and so on. My birds that I will sell will be selected AFTER I pick the best ones that will stay in my breeding program to improve my lines.
This is the biggest difference. Small operations, more or less (there are always bad apples

plan to improve their stock over time while hatheries only care if the birds moderately conform to the standard. If it kinda looks like that breed, then they can sell it as that breed. Some breeders sell pet quality birds and are up front about this. Production birds, for instance, can be bred for different reasons than conforming to the APA standards. They are still breeding for things that are important to their flock...egg producing or meat etc. That is entirely different.
Hope this helps
edited to add: I believe a breeder becomes a hatchery when improving their birds is less of a concern and the profitability is more so. I think a "hatchery" can still run without all these certifications and licenses. A hatchery may just consist of 15 breeds in someone's backyard. They may even call themself a breeder. It saddens me to hear people talk about buying hathery birds to raise and sell to buyers whom, most likely, believe they are buying better quality simply because they are not buying from a "hatchery." It is a fine line but notably different when considering what motivates the operation. One more thing
don't want to knock all hatcheries. There is supply to fill everyone's demand. Things I look for may not be important to someone else.