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First thing...welcome to BYC!
The difference is exactly what you said....a breeder practices selective breeding and only breeds the birds that meet the APA standard for that breed and color variety....or at least as close to that standard as they can get, while hatcheries breed and hatch for quantity, not quality. No, it is not very likely at all to get a good quality bird from a hatchery. Your wyandottes will be wyandottes, but a lot of hatchery wyandottes are not marked well and don't have the correct body type. That doesn't mean they won't be good layers and nice birds tho.