How to set up Time Machine backup for two macOS disks with third data disk?
Time Machine backups are organized by machine directory, then by snapshot (date&amp;time), and only then by backup source (see the section on "backup structure" in the man page for tmutil). I might be wrong, but I would expect your Sierra and Mavericks installations to be considered separate "machines", even though they are running on the same physical machine. I'm not sure whether Time Machine is smart enough to realize that the backup sources for these two "machines" are the same, and to use hard links between them to avoid each machine directory to include completely separate copies.

I think the simplest thing to do would be to set Time Machine on Sierra to backup all volumes except the SSD with Mavericks, while setting Time Machine on Mavericks to only backup the Mavericks volume. Or some variation on this of course, like backing up everything using Sierra and turning Time Machine on Mavericks off.