Pretty fricken complicated dudes. I say take out the harbor from trading company, and make it give a courthouse type corruption reducer in every city.
call it Customs House, and make it available ONLY with the wonder.
Although, with an advantage that immense, it might be a better idea to reduce trading company to small wonder status, and make it dependent on an invisible resource in/near the capital of civs that had colonial empires (russia, france, england, netherlands, portugal, germany to an extent, spain, china maybe, japan maybe, usa maybe).
That way they can build colonies without having them be megasucky.
I still think the best solution to the problem of hyper expensive settlers is making the palace produce them at 20 turn intervals, but that would create plenty of problems on its own.