I don't see the problem. Trade Routes are a complete nuisance and I never use them. There simply aren't enough slots on the route. It is so much easier to send the solitary waggon on a fur collecting expedition. Then having dumped all the furs in the Customs House city it goes off collecting sugar. Factories and Custom Houses go together so I never have to move manufactured goods. I might have a second waggon which moves timber, tools and guns. Since each of these is a bespoke journey, then trade routes are not appropriate.
I don't like paying tax and always run 0% tax rate. I have never considered letting the tax rate rise. Even the cost of losing 100 tons of silver is recouped by the tax on a single City of Cibola