I can't speak for the 2006 model(s), but I test drove a 2007 Matrix a few months ago, planned on buying it, got shafted by the dealer and instead got a 2008 Vibe this past weekend. The two cars are nearly identical on the inside, but the radios are different. In fact, the one in the Vibe is the same one that was in my 2001 Grand Am, except black instead of gray
However, I only saw the stock radios in each model, not the upgraded ones. But if you look at the pics on Toyota's site and on Pontiac's site, it looks like even the upgraded models are different. Whether the difference is simply cosmetic, but offers all the same features, I'm not sure.
Not that those pics would offer much help, but your post makes me think you know that the Matrix one either does or doesn't have what you need, so I figured I'd throw what little I know your way just in case.