I'm pretty sure settlement income includes corruption loss. If you look at the settlement details, under income, say for Bologna, you see:

Income:
Admin = 47
Trade = 133
Taxes = 617
Farms = 442

and in the "negative row" you'll see corruption = 83.

The settlement income is reported as being +1156.

You'll find that 47 + 133 + 617 + 442 - 83 = 1156 exactly.

Furthermore. I went and added the incomes of all the settlements while keeping them separated by category. The numbers matched exactly with the financial overview numbers, i.e. adding all the income from farms yielded 1877, as on the financial overview. Corruption and other income (192) is gotten by adding all the "admin" incomes, and corruption loss is gotten by adding all the negative corruptions in the settlements.