It's quite possible to make the stock drills extract MetalOre, but there are a couple of problems with it:
I prefer to work with mass rather than volume, so that's how EL's augers are set up (custom extractor module derived from the stock one, but with custom recipe handling). This means doing a balanced config for stock drills will take some skull-sweat.
Stock drills are suited only to gaseous and liquid resources: how are you supposed to get rock, even powdered, up that pipe?
Yeah, the auger is not the nicest thing to look at, and it doesn't fold away, but it does at least look right for the job.
As an aside: I don't use the stock system at all (minus the fact that the auger will automatically pull MetalOre from the stock system). I much prefer Kethane's mechanics (part of why I took it over) and I'm quite happy with using multiple drills: kethane drills for Kethane, augers for MetalOre.
I really need to get around to doing a tutorial series, but of all the bases I've made (8 now, I think), I have flown augers (or even smelters) out to only one: the very first one. At all other bases, I built everything on-site. I even usually build better workshops on-site. I have launched exactly two workshops (the big blue thing) into LKO, but built many stations. When I fly a good workshop out to a base, usually it was built in LKO (my current Jool mission is an exception: didn't have time before the launch window to build the engire ship, so I flew up a workshop to build the Jool ship.
In summary: all you need to start a base is a survey station, some survey stakes, and sufficient RocketParts to build a tiny auger (0.5328t), tiny smelter (1.5t), and a rocket workbench (1.5t), plus a few extras (batteries, solar panels, legs, KAS connectors).
The smelter has built-in storage for MetalOre, Metal and ScrapMetal, you already have storage for RocketParts (though you will want to build more), and with the above, you will have everything you need to get a fully functional base up and running.