Contrast that to a large dairy operation. Several hundred cows mean higher pressure to get through them all, and a higher chance that the farmer misses something. Half of all cows are in herds of over 900 animals, which means that many operations are now completely automated, removing the visual inspection that a farmer in a small-scale operation performs. That milk is then sent to a milk processing facility that may process upwards of 100,000 gallons per day. Any bacteria from one cow can and will be mixed with the milk from multiple other farms, and can potentially infect tens of thousands of gallons.
Anecdotaly, we have several friends who cannot digest homogenized milk, but do well with raw milk. We are not sure if this is due to the makeup of the milk fat or due to the (usually harmless) microbiota in the milk.