There are much better way than his, even not running linux on PC(but if one can boot with ldots' xboxhdm, that is the best option). I can outline a simple procedure :
1. run a version of linux(ldots' ltools for example) on a modded Xbox.
dd if=/dev/hda51 of=/tmp/cdrive.img bs=100M
2. either zip it or copy it directly to the PC through ftp
3. go to
http://www.cygwin.com and install it, make sure to install the "dd" package
4. now hotswap as usual, then start the cygwin bash shell and do the following :
$ dd if=/ftp/cdrive.img of=/dev/sda seek=4501 bs=512K
I am not too sure about the 4501 number and bs number(need to check). sda is primary, sdb is slave etc.
The same procedure can be used to duplicate the whole disk. The new disk is now modded too. Now just make sure the kernel likes whatever modd is there. But like you said, blindly doing this kind of thing can be harmful but it is a way to rebuild a Xbox HD(from another working modded Xbox), all under Windows(not 98/ME as that won't work). The same procedure can be used to make a zipped copy of a virgin C: image when first running a game save and save it.
I am not sure if ATAPWD is a windows program or not. If it is, one can even do this to upgrade a HD, all from within Windows as just lock the disk after the mirroring and viola, time to install.
So for people who can run xboxhdm, use it(together with ldots ltools). For those who feel alienated by linux, this can be an alternative.