Okay, hear me out.
Along with the extra throughput, unincorporated states with colonial exploitation have lower wages, lower mapi, and no institutions. Which means they have lower SOL and literacy (which doesn't affect research speed because they're unincorporated). Which means that the birth rate is higher, because the birth rate lowers with higher literacy and SOL above 15.
Obviously, if you have a large population in a state numbering into the millions, incorporation is a must. But if there are rural areas (like most of Russia) with resources potentials, like wood and mines, would it not be better to leave them unincorporated in order to farm pops and resources? Yes, -10% mapi from being unincorporated makes those resources more expensive in your market, but late game when you are hitting 4-5 billion gdp (even when playing low infamy) you are constrained by raw resource amounts (iron, rubber, etc.) than anything else, which throughout will help with. Having Africa and South America unincorporated to produce more rubber for my Ford Motor Company, for example, makes sense.
Because it is inefficient to build manufacturing in these unincorporated states, your pops will naturally invest in building manufacturing in urban areas and automatically downsize owned manufacturing in rural areas. As there are less and less jobs in the rural areas, this unemployment will lower migration attraction in these rural areas, which makes these unemployed pops move to higher attraction areas, the urban areas where there are more jobs. They will then become affected by your institutions and become richer, which contributes to consumption and thus your gdp. Then, the cycle will start again, as the pops that remain in the unincorporated areas will continue to have a higher birth rate.
Because your research rate only counts literacy in incorporated states, and because lower literacy and limiting SOL to 15 increases birth rate, using Colonial Exploitation to find a nexus where you can have the best of both worlds and benefit your industry at the same time through increased throughput just makes so much sense.