You can still get your PC iPod to sync with your Mac library and you can download the Windows updates on the Mac and then transfer them (using the iPod even) to the PC just for updates, which aren't that common anyway. You'd just have to make sure that when you plug the iPod into the PC, you don't let it sync the PC's library.
But if this sounds too hard, fair enough. I can't find anything on Version Tracker though, sorry. 😱