MPC is not really an Embbed APP in RR. To make it a little less problematic, I insert MPC's window within RR's window -- this takes away the possibility to send keys directly to it.
To prevent issues, RR always copies a "fresh" INI for MPC to use.. this file is actually mpc.ini (not mplayerc.ini). If you run MPC and assign hotkeys, they'll only work if you copy those hotkey definitions into mpc.ini. Even so, they'll likely only work using the keyboard.
I can most definitely make support for a DVD skin. But if you tell me what exactly you have in mind, I may just do it already.