how?

there's additional operational cost in the form of energy used if you have far off resources being harvested. and the transport shuttle has to go get the goods, which increases cycle time a little. i have less than a dozen games in but i definitely didn't feel like I was managing the logistics; that moving stuff around was an issue or concern. there's a lot of different resources but they all roll up pretty automatically wherever they are without thinking about it. that was my (limited) experience.

I agree. It models it (which is more than most RTSs do), but it adds a fairly small amount to the gameplay (mostly location becomes important, it gives another element to the core supply and demand mechanics, and it gives value to one of the technologies which basically just eliminates the cost entirely).