I just tested the autoload method of an Add-In ArcMap Application Extension. That mode causes the extension to automatically fires up at ArcMap start. From there the extension code could examine the configuration of ArcMap and if needed reconfigure ArcMap to include any buttons, tools, toolbars, menus, commands, dockable windows, etc that the programmer needed for their users. Admittedly, this is not as easily done as creating and storing a template map, but it does provide at least one method for acheiving the same end result that is not document based.