The settlement quality Racially Intollerant says:
Racially Intolerant: The community is prejudiced against one or more races, which are listed in parentheses. (Members of the unwelcome race or races must pay 150% of the normal price for goods and services and may face mockery, insult, or even violence)
There is no effect on the settlement only on visiting PCs or NPCs. Was this supposed to be a settlement disadvantage? If not what should its effects on the settlement modifiers?
That it makes 50% more money when those races are present?
I would add "and cannot gain positive benefits of any settlement modifiers to skill checks" to the effect. Not really sure it's a disadvantage, but it would have a broader impact.