From my experience I can say that the subject that you get from a colonization charter and from Civilizing Mission are pretty much the same.
Btw after the colonization finishes, the company charter is no longer used up, but you can't disband the company anymore.
Some non-obvious benefits of colonial subjects include the fact that for them state incorporation is twice as fast, so they can incorporate new states in 10 years instead of 20, and I think the ones that you release from Civilizing Mission decisions already start with all states incorporated.
Besides that, they start with the Extraction Economy law, giving a small boost to the resource buildings throughputs.
