Zenphoto requrire that setup be run before anything else. Setup creates the tables, so they should be there for the restore. Restore will, of course, restore rows of the tables.
If the Zenphoto releases are different, then there may be some tables/fields that were backed up but have no place to be restored.
The released version of backup-restore does not take that into consideration. There is a ticket on this. Attached to that ticket is a backup-restore that will handle missing elements. But it will not be released until after 1.2.7 since we are in development freeze now.
There is no problem with the rows of missing albums/images so long as you do not do a database refresh. That is when the cleanup occurs.