by Justin Almeida.
Almost a year later, anyone with any suggestions from my OP?
I dug around some more and I just can't fathom why there isn't more demand for this sort of option during the restore process.
I did find that if I restore my courses in reverse order of how I want them to appear, then move the newly restored material to the bottom section and ensure that there's an empty section above it, that the next time I restore material it will be dropped into the empty section.
This still creates a gradebook nightmare as none of the categories from the backup are carried over after the restore, but it's still less work to have to perform!