Ok good questions..
First, the option about saving backups is not stored in your regular launchbar file.
The backup option is stored in the LaunchbarCommander.MCP file, which also tracks other global options (and keeps track of what launchbar file is open).
If you write protect that file, the only problem may be LBC may complaining about not being able to save its file.
The selection of that file is somewhere around:
CheckBoxBackupOnMaintenance and ComboBoxNormalBackupFormat.
LBC would be quite happy to let you store the .mcp file in one place, and the .mcf file (the file containing the actual definition of a specific launch bar), in a separate place. Perhaps the thing to do would be to sync the .mcf files and leave the .mcp file (which has very little options) unsynced.