The overall income number will be fine. But if you go into the financial advisor to see how it breaks down you'll find the sub-totals don' add up to the income number any more, because you applied the modifier to the total only.
Instead of changing the total, if you change the inputs (so the amount generated by each source - buildings, trade routes, taxation, ...) it will give the same effect on the total, but also show up correctly for all the sub-totals. I'm not sure off hand how many basic input values there are, but it's order-of 5 or so I think. Note that this will also cause the numbers displayed in the city screen and the building hover text to b correct (i.e. - adding a building with a hiver text saying I will give 2 gold will result in your total gold/turn going up by 2, which right now is not the case because you apply the modifier to the gold-per-turn but not the building hover text)