About the iPod app -- I have a Pioneer unit that I can control my music from even when it is set to control music from the iPhone. For example, I can still change tracks from the deck while Navigon is running. Also, I have the double click of the Home button set to bring up iPod controls which also works well.
question: did you connect your iPhone via usb to your pioneer? if so do the voice commands also go through your stereo and onto your car speakers along with the music?