I would say yes the mines have to be worked to get that gold, same as any other tile improvement.
You are right about that builder. My biggest decision in my first game (which will be Mali of course) is do I go scout first or builder first? I suppose it may depend on how many turns to research mining. Which will be the first tech researched by most people I imagine. After that do you go for astrology for a religion or say animal husbandry?
Ideally I would love to have 2 grassland hills to mine at the start, even if I had to sacrifice some food/faith by not settling in all desert.
I think early game they'll be similar to anyone else - you just have to know that you're getting ~1-2 production less than a normal civ, and that you can't throw a mine down to speed up that settler production. And you also have to realize that they do get the production bonus from quarries, and they do get them from pastures.
So I think I'm still going to research for whatever resources are around me. I'll still go slinger-builder early on. But I'm also definitely more likely to move my settler by a tile or two to set me up better in the desert, and if I do happen to have lots of desert around my starting city, thus giving me lots of free food, then which tile I work certainly will change. The interesting questions will come up if you have a food tile that you can work in the first ring - do you work it to grow super fast, or do you need some production early? If I'm growing faster and have lots of desert around, do I have to be more aggressive in buying tiles?