Website says "To defragment your boot volume, you need to boot from a different volume (except for on-line defragmentation feature)."
What does this mean?
This means you cannot boot up on your main hard drive and be able to defrag it. iDefrag has a utility to make a bootable CD which you'll need to use if you wish to defrag it. I have cloned version of my internal hard drive and so I can boot up on that as well. The OS locks the boot volume preventing write access to operating system folders and various other files which is why you need to boot up on some other drive (be it an external hard drive or a CD).
As for your other question regarding cloned images defragging for you. Yeah its possible but products like Carbon Copy Cloner use a block by block cloning, not a file by file cloning process so if the blocks contain file fragments you'll get those fragments back again.