I've got my Mk II wired in to my home stereo and it mostly works using my Harmony 720; the biggest issue I've got is powering on/off: when the Harmony powers up the RioCar, it also changes the Source to Auxiliary. This doesn't happen using the Rio remote or the buttons on the player. I'm pretty sure the issue is that, I think, the player is looking for a long press and the Harmony is sending a short one (the Source and Power buttons on the Rio remote are one and the same).
The other issue is that when I use the Harmony to power everything off, the RioCar doesn't power off. It doesn't change Source/input, either, which I would have expected, given the issue powering it on.
Has anyone fought this fight already? If so, would you be willing to impart your wisdom?