Well, if permissions are set correctly in the share, then they'll be visible, but what are you planning to do with them? In general, it's a good idea to avoid doing anything that will potentially screw up your backups. If you need to back up these to another location, then you can do ZFS replication of your time machine dataset to a separate system.
If you need a file-based backup, then you can use any of the multitude of 3rd party tools that do this (or just rsync).