First I assume you are selecting HFS not HFS+. You also have to make sure the partition map is legacy as well. In Toast there is a tick-box which must be selected in order to make the disk bootable. Not sure about Disk Copy, or others. As I recall this was a pain at the time and likely still is.
Emulators have a significant amount of leeway in what they allow you to map because they are not using an actual disk drivers, but a substitute which allows you to use whatever devices are on your machine, most of which can read numerous formatting the machine won't. The emulator still uses the data authentically. However, Basilisk II which doesn't exclusively emulate specific hardware, unlike Mini vMac which will not let you run any software the real machine won't.
If you haven't already done so, make sure you make some backup floppies with the proper CD drivers in it should this ever happen in the future.