I upgraded all settlements to level 3 after the patch, since I was carrying a huge food surplus. I still think some buildings need a reduction in their penalties, mostly level 4 buildings and specifically the ones that trade food for public order and vice versa. The bonuses for most minor settlements are not worth it versus the penalties they bring, at least compared to upgrading the provincial capital.

I still prioritize food buildings in 2 and 3 settlement provinces. I still prioritize the food and public order temples over the others.