Great idea, I'm in favor

If you compare modern nations budgets, you will see that docking fees and all that are only a very small part of the income. They are negligible and since the economics model of GC2 is a very big abstraction, I do not see any reason to complicate it on behalf of a not noticable gain in game mechanics. Do you really want to set docking fees for every starport? I do not want to.

(In the current model, the money "going through" the starport actually is taxed on the side of the customer.)

The customer is paying taxes.
The point is, that all taxes are added together and result in "taxes". There is no distinction between private consumer taxes, private income taxes, corporate taxes, fees and fines or even pay-back of government investments. There is not pension fund system, no health insurance or unemployment insurance. It is all amalgamated into the numbers we see in the economics screen.

A game always has to have a certain level of abstraction and the larger the scope of the game is, the larger the level of abstraction. The starport building is not a symbol for a starport as you see it, but a symbol for a large governmental wharf. Besides that edifice, every planet has a lot of private or economic wharfes and starports. The one you build just gives you the ability to build ships. It has nothing to do with ships being able to land or start from that planet. After all, you can build trade routes to planets that have no starport and you can land and start from planets without starports.

To summarize my argument: If any change is necessary, we should rename the starport to "military wharf". The commercial income generated by trade is already considered and it is considered elsewhere (commercial buildings, trade routes and general tax income).