Anybody can sell any animal to pet stores. You don't need to be USDA certified. I'm thinking you are supposed to be USDA certified if you sell over X amount of money to pet stores a year. Or it might be if you sell X amount you have to declare yourself a broker. I can't remember how that goes.
There are different classes of licenses depending on what you do. For instance breeders who sell just to distributors are Class A. Distributors are a different class as are exhibitors. Fees are paid based on your dollar volume although you also have to track number of animals sold.
Here are some stats from their site.
http://www.aphis.usda.gov/animal_welfare/inspections_type.shtml
And if you go to the bottom of that link, you can review reports for people that are USDA certified. They're public information.
I believe it's still current that you must have a USDA license if you sell over $500 per year in animals to pet stores and/or distributors. For chins, $50 would be on the low end for what a distributor would pay, so by selling just 10 chins, you would need a USDA license. Distributors are regularly inspected as are breeders (at least once a year but also more often in unannounced inspections). Distributors must show that anyone supplying them more than $500 in animals is USDA licensed, so they'll require it of their breeders -- and they'll rarely work with small breeders. Responsible pet stores will also ensure they buy from USDA licensed breeders if they buy more than $500 a year, but not all are responsible.
And at least in Southern California, the distributors have the animals shipped in (for the Petcos and Petsmarts) or pick up from local breeders (for many independent pet stores). Once the distributor has the animals, they transport them via air conditioned panel or other vans to the various stores on a given route. The route will generally run once or more often twice a week. Stores place orders based on need.
Petsmart has been the exception. Our animals have been trucked in by Rainbow World Exotics in Texas. The trucks leave that facility and go on multi-day runs hitting our stores well into the run. I'm told they have switched to a rather poor local distributor instead, and that distributor has many if not most of their animals shipped in by plane.
And yes, your big distributors merge animals from dozens of breeders who have sent animals to smaller distributors who then send them to larger distributors. You can see the networks through some of the CDC reports when there are disease break-outs that affect humans.
I've been to a number of smallish distributors (mostly Petco or independent distributors), and the best of them keep animals of different species apart and even keep animals of the same species but from different breeders apart. Then, if there is a disease breakout, they know the source. Your distributors range from very good to very poor just as your pet stores do.
On the delivery trucks, though, you will see all animals kept in separate bins or boxes, but disease could spread. Expect giardia in any animal coming from the commercial breeding system. It just won't flare up until the animal is stressed.
And no, even the small local distributors who buy from local breeders and focus on quality animals don't get pedigrees and don't track which animals belong to which pedigrees. I'm told there are a few pet stores who actually fly in their animals from top show breeders (not in chins that I know of) and request pedigrees on each animal. Those animals (hamsters in the case I best know) are sold for a premium, and the purchasers tend to really value quality. Their volume is of course low.
Linda