FC probably doesn't come with any proprietary software either, so you'd have to update your repositories or build your own RPMs to get stuff like official Nvidia or ATI drivers, Flash, mp3 decoding, and other formats. I'm betting Red Hat comes with that already.

All Linux distros run on the standard ext3 fs (good for stablity) and reiserFS (good for transfering big files, less stable), so you won't have a problem there. Directory layout should be the same too; /etc, /lib, /opt, /proc, /usr, etc. As long as you use the same RPM build it should extract the files to the specified directories.