Industrial operations have industrial scale problems that require much higher standards. The local butcher might not scrub the floor and walls with the same industrial anti-bacterial detergent, but he's also not running hundreds of cows a day through the space. The local farmers don't pre-emptively administer antibiotics to their herd; the CAFO operation that feeds the industrial slaughterhouse has to cram antibiotics into the cows to keep them healthy enough to slaughter. Comparing the two directly is very misleading.
The way the butcher explained to me, it’s not so much the volume that’s the problem, it’s the time between cleanings which gives microbes time to multiply in ideal conditions with lots of nutrients from blood and optimal temperature. Any crevice that’s hard to clean becomes a focal point for contamination and it doesn’t really matter if you’re butchering one cow or a hundred, because if you leave that biofilm there for even a few days, it can grow enough to contaminate future batches.
The other side of it is that many forms of contamination sporulate, so short of using a powerful surfactant to wipe it all away, the spores will survive basically forever until they hit growing conditions.