I’m not sure how to answer your question as I don’t know how Google Apps works for a whole company/department. Maybe there is a ‘super-user’ that sees all the personal folders of the individual accounts. If so, maybe in that case, you could create a rclone remote for this super-user and copy everything in one swoop. I haven’t used it for your use case (I’m not even sure what that is exactly) so I can’t really be 100% sure it serves your purpose. I believe rclone sync command uses something like the rsync, so I’d expect the operation can be interrupted and will continue next time it starts
Remember that rclone does simply a copy, it’s not really a tool for backups. You may also want to check other options, like Retrospect or Cloudberry. Again, I’m not sure they work with Google Apps but they’re worth investigating if you need backups.