The Petco I used to work at, where BF still works, is very well taken care of... because he's in charge of the reptile department.
Some Petcos are considered "reptile magnet" stores, which is an experiment in more specific marketing. I got my enchi male from BF's Petco, and we got our male pinstripe from the store a little north. This store has sold Mojaves, Pastels, Spiders, Pinstripes, Enchis. It currently has a Biak GTP and an ARU GTP.
The reptile supplier for Petcos in the Pacific Northwest is called California Zooligical, and they're no different from a large scale breeder such as LLL reptile or Outback. Not as much hand's on, but they do breed some of their own animals, but a vast majority of them come from local or private breeders that specialize in one area.
Petcos in different areas across the country have different suppliers - some share suppliers with Petsmart, some don't. Some suppliers take better care of their animals, and more importantly, some stores hire more competent employees than others, but you can't really say or suggest a morph from Petco is automatically going to be worse quality.... as they ultimately come from the same types of breeders that might post on this forum.