you wouldn't use union mounts to mount /, /opt, /opt/whatever
you would use union mounts to mount three different filesystems on /opt/whatever
and yes, all your writes would land in the top filesystem.
to work on a lower-level filesystem you would need to unmount the layers on top of it, and to get back where you started you would need to remount the layers above.
if you write something on one filesystem, but decide you want it on the filesystem below that, you would need to unmount the top layer, mount it somewhere else, and move the file from one filesystem to the other.
I don't understand why you think you would need to mount them in a different order.
if you have dev/1 over dev/2 and decide that they should be in the other order just unmount them and re-mount them in the other order.
your filesystem is already dependant on the order that you mount things today.
if you mount /dev/1 on /opt and then mount /dev/2 on opt you will see the files in /dev/2 and not /dev/1, if you mount them in the other order you will see the files in /dev/1 but not in /dev/2