That would involve 'teaching' the firmware to regognize (and destinguish between) the two partitions. I personally have tried this (not with the default and linux, mind you) and itunes regognizes an ipod, and osx notes two disks. I don't reemember actually trying the ipod, but I assume that It would regognize the first partition.
I'm pretty sure this is what happened, but it could be that itunes regognized two ipods , rather than one. I doubt this though. I'm relatively sure that itunes can only address one at a time, for the two theoretical 'devices and disks' are connected through one device and are not expected to be.
I'm guessing we are talking about IPL, and not a Linux-formatted ipod?