According to the description, prelates improve the collection rate by 40 percent. But it seems to be closer to 20 percent. Farms supported by prelates give about as much food as English farms.
40% is a collection rate bonus, not the overall change in resources gathered. They will spend additional time walking back to the mill which reduces the effectiveness of the bonus.
Additionally other farming bonuses and eco upgrades may be confusing your test. It could also be that the prelates aren’t consistently buffing all the vills.