Yes, the cleanliness can vary based on the outfit and the tech/facilities tends to be lower. However, there are not 100s of animals being ran through the same grinder. It doesn't seem like there are any real tests being done to each animal by the inspectors.

So facility risk seems similar or higher for the local shop, depending on specific people running it, but animal-bourne risk seems higher at the packing plant, which seems to be the more likely vector to me anyways.

No data on that. But qualitative experience shows the local farmer/butcher has much nicer/fresher looking/smelling meat than the Walmart.