I use my iPod all the time, its just connected via the headphone jack on the ipod and plugs into the Video 1 jack on the radio.
you can still use an iPod, or any other sort of device that has a headphone jack. you just need to connect it via the RCA in jacks on the radio, you only run into the problem if you use the special Pioneer ipod cable that costs extra.
the problem stems from the fact that there is limited screen real estate, and i thought that probably not to many people use the special ipod cable, and would want the bigger clock.