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I realized recently that you don't need to build a gold refinery to build gold miners. Similarly, you definitely don't need a lumber mill to collect wood.

Then, what is the purpose of these buildings? Are they just useless?

According to Coloniae, these buildings "collect & refine" certain resources. Does this have any beneficial in-game effect, or does it just mean the same thing as "storage"?

i.e. is there ANY reason to build a gold refinery instead of an extra raw materials depot?

you are correct. you can just make do with raw material storage without having to build gold refinery

Mainly, they operate as drop off locations for rovers if you don't have the correct storage setup. They also make atmosphere, and that's pretty useful in late game. But yes, they don't really add resources to the game, but they still do have a purpose.