I worked at the other Pet____ store , so I'll throw in a couple of cents.
These stores do get their animals from mills. Unfortunately, animals are often shipped regardless of the store's on-hand count when there's surplus. My store occasionally received animals that were supposed to have been phased out, and it wasn't unusual to have way too many of something. We had pretty compassionate management that allowed us to set up overflow tanks in the back instead of cramming/mixing the displays, but ultimately, at store-level the employees have their hands tied in regards to proper care. A manager that cares might forward your complaint, but the best thing to do would be to contact corporate about improper set-ups and misinformation (note that employees aren't actually required to know about the animals, they just have to know to hand you a pamphlet, which is often full of bad info).
I don't like to convince people one way or the other after being on the "bad side", because it's complicated. Even if the store wants to stop stocking an animal due to disinterest/deaths, they'll still receive them if the DC has extra (there was a wide-spread issue this summer of stores ending up with 80+ koi because the DCs just had too many and didn't care what the stores were meant to do with them. It happens with guinea pigs, hamsters, and certain reptiles all the time, too.) However, if you buy some of that surplus, it won't necessarily be replaced (by that I mean: if the store has 5 lizards when they're only supposed to have one, they should only receive a single lizard once the five have sold).
The animal's health is a gamble, but my chain (not sure about Petco) had a policy that if the animal needed medical attention in the first 14 days we'd buy it back, take it to a vet, re-hab it and offer to let you re-buy with no medical expenses on your end (I promise they don't just throw your animal out and get you a new one, that surprised me honestly).
In the end I think it is just a moral decision about supporting the business or not. Buying from hobby breeders is always best, but not without risks (especially now- I spent the first half of this week fighting FedEx about a live animal package they decided not to deliver...). I'm not trying to defend chains stores, either- I personally prefer to support hobbyists. I certainly can't criticize, because I took my little lady with me when I left that place ?