In Clonezilla, one boots OS-1 (Clonezilla) on Drive-1 (USB stick) in order to make a full, restorable image of Drive-2 (which may contain OS-2) on Drive-3 (the backup drive). One does not need any permissions or "root" on Drive-2 or OS-2 in order to make this copy. In fact, one could perform this procedure on any drive at all, including your drives, without knowing any of the relevant passwords!
Question #1: How can I use free software on OS-1 (Linux, Windows, etc.) to make a full, restorable image of Drive-2 (brand new, untouched Android phone), including ROM, bootloader(s), and any other sections, partitions, etc.?
If you believe the answer is, "You can't," then..
Question #2: After I have rooted, how can I restore Drive-2' (the rooted and thus altered Android phone) to its original state, Drive-2 (brand new, untouched Android phone)?
If you believe the answer is, "You can't," then..
Question #3: Why should I not worry about this?
It seems odd that one must alter Drive-2 (rooting process) in order to make a copy of Drive-2', but it seems like ClockworkMod's NANDroid images (and others) do exactly this by requiring root. Perhaps I am simply confused.