I've never tried to copy an original disc, but I tried a few .xfd images and they always worked on my real machines (5.25 and 3.5").
How can you do that ? The 3,5 floppys boots on a compact ? Explain all the process for make the copy in 5 1/4 and 3 1/2.
I really think, to make copies, using xdf 2hd or dim tosec images is possible. Perhaps some are desprotected like pc games or amiga games in his day, but if it runs in emulator it must run in a real machine.
The deal is to find a pc floppy drive 3mode compatible, configure it soldering or modifing jumpers (must be configured to write 3,5 disks at 360 rpm instead of 300) and activate the 3mode capable in pc bios.
I discover samsung sfd 321 b is a 3mode capable drive, but it must be activated to be a real 3mode. This guy says how is the modification. Samsung sfd 321 b drives are common now, and easy to buy on every computer shop or ebay.
Look at this post: http://majzel.blogspot.com/2009/04/converting-from-8-to-35-inch-floppy.html
With this and using xfloppy, or other utilities in the pc in pure dos, it must be sufficient to make perfect clones of disc images, because looking at the takeru discs photos, are normal floppy discs, and I don´t think are special drives or special discs.
Some months ago, argentinian guy "el piloto" discover that amiga floppy drives, are the same as pc ones, only changing 2 wires :http://www.retrocomputacion.com/cgi-bin/foro/YaBB.pl?num=1169698625
Other examples of using other media in other machines is amstrad cpc 6128 for using 3 1/2 drive instead 3" ones.
Resuming, I think is factible, but I don´t have the compact x68000 to try it, so, anyone of here that have one, and want to try this method, I think have all the info to try it.
1. Buy and Modify samsung SFD 321B, 3 1/2 DRIVE (I think other models are capable, but...... how ? )
2. Activate 3mode support for this drive in bios (drive a:), if your bios have this option.
3. Use a normal pc with win98 and xfloppy proper installed (see readme of xfloppy) or similar programs (octocom, etc) and write xdf tosec image to a 3 1/2 - 1,2 mb writed at 360 rpm.
4. Try disc in a x68000 compact and if runs discover the holly grial XD
If this runs, the other deal is to make run externally a 3,5 floppy drive, but this is other history..............