So it appears Apple allows the dock input to be used simultaneously with the headphone jack output, but not the other way around.
That's right. The iPhone (and 2G iPod touch) can tell the differences between headphones (or a stereo connector) and a headset (a four-conductor connector). When the headset is used, input and output are routed through that single jack. If headphones are used, the iPhone looks for input from another source, so you can use dock input and headphone output.
Thanks for the pointer to ThumbTacks. Should this microphone be oriented vertically for EQ measurements?
The microphone is omnidirectional, but the iPhone (and your hand) will obviously affect that. A vertical orientation, then, should be fine.
Ben