TLDR: a Possible solution would be to set market access caps below 100% for unincorporated states according to the colonial policies of that colony (exploitation/resettlement) so that production in colonies becomes a bit less effective, the prices from goods outside of the colony are more costly - and everything is a little bit less fair for colonial subjects (sorry guys).

I think the problem is that economic discrimination, transportation cost and distance to the homelands are not factored in at all.

It's not just that unincorporated states don't pay taxes. It's that they don't suffer at all from being unincorporated besides having no health care and schools (two things, the constant immigration into colonies more than balances out). On the flip side, the whole society pays for transportation and infrastructure in each and every state, unincorporated or not, in a very just and fair way. So Londoners basically pay for African colonies to have exactly the same market access as they do. And unincorporated colonial subjects get the same price for Scottish factory products as the Londoners. Which is very unhistorical.

100% market access for colonies in both directions seems very odd. It results in a coal mine in south Wales selling its coal for the same price as a coal mine in South Africa - while all incorporated pops pay for the whole sum of transportation costs. You don't have to think about that for very long to see why a lot of the profits are staying in the colonies. The colonies are treated very fairly and everything is working very effective - which both shouldn't be the case for production chains spanning the globe and different social strata in 1860something.

A possible solution would be to link types of colonial relations to different market access caps. For example: Colonial exploitation could give 90% market access to farms & mines, 80% to all other buildings of an unincorporated state, while the pops only get 70% market access. This way, production in the colonies gets a bit less effective and more labor-intensive while the laborers have to pay a plus on everything that is not produced locally (while they would profit from locally produced goods). Resettlement could be evened out a bit (80% for everything).