Ok, I asked a few guys around here and this is what I was told:

The Fraunhofer encoder uses joint stereo to encode the MP3s. However, at a certain bitrate, it switches over to using true stereo. I couldn't seem to get a definitive answer on what that bitrate was, although I'm sure it's something like 192 or 224.

But, there is no actual setting to turn it on or off. For that kind of control, I'd recommend LAME.