i used an ipod dock like thing for a car...one that plugs into the cigarette lighter and has a built in fm transmitter, and that was it. it didn't feature any kind of remote control...i will tell you, that like external speakers, this worked just fine with rockbox. from what i can tell, the audio-out pins on the dock connector aren't sofware dependant, but rather they seem to be wired directly into the DAC (or somewhere similar) of the ipod, before the hardware EQ i believe.
so, to answer your question, as long as you don't want to use any kind of remote control features, the fm transmitters that interface into the dock connector work perfectly.