Sorry but I don't get what you're trying to say here, how is this a "potential spoiler" and what confused you specifically? As you rigthly point out Theron says:
"She’s the machine that runs the machine and is in charge of sending Prometheus into space."
Which raises the question. But she then she goes on to say:
"She runs a tight ship, but you can tell that she’s going to be a problem. She’s an enigma; your quintessential bureaucrat making it hard for everybody."
...the answer is a play on words and right there my friend