I've never seen 2 of the same Commander up at the same time, and I spent a significant amount of time there as well keying up for the Emp. Comm 1 can spawn anywhere on the first floor, Comm 2 can spawn anywhere on the next floor. Typically, fighting in the room around the tube is your best bet if they aren't already up. With a good enough group, you can clear the room around the tube on the first floor, then bounce up through the tube to the next floor and clear that room. That way you can try to get both Comms at the same time.
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Some people are like slinkies, they aren't really good for anything, but they still bring a smile to your face when you push them down the stairs.