The simple modifications that Community Auth makes to extend CI_Session are not likely to interfere with the way that you would implement bootstrap-session-timeout into any non-Community Auth project. Have you tried testing bootstrap-session-timeout in a plain CodeIgniter install?
As far as I can tell, your question really does not have anything to do with Community Auth. You might create a new thread for help, because you're not likely to get a solution when people think this is tied to Community Auth.