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After more research, I think I have a good solution for this issue.
One idea is to have a "Users" symbolic link on the "boot" drive (SSD) pointing to the Users folder on the "data" drive (HDD).
If these two drives are backed up to separate partitions (on an external FW HDD), I can simply have SuperDuper! run a shell script at completion of the "boot" drive backup which replaces the "Users" symbolic link on the "boot" backup with one that points to the Users folder on the "data" backup.
An alternative would be to leave the Users folder on the "boot" drive, but replace my home folder with a symbolic link pointing to the actual home folder on the "data" drive, and use a similar backup plan.
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