There is a fairly complete description of commerce in the Datalinks. The only thing I have observed which behaves differently is that crawled energy is not included in the commerce calculation. In this case, working an energy-rich square within the base radius is better than crawling it.
Usually, giving a base to a surrendered faction is less efficient than personally taking care of it. Sure, you'll increase commerce in another of your bases, but by making the base specialist-heavy, you'll get more lab and econ output.
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Why doing it the easy way if it is possible to do it complicated?
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