This is a demo how to encrypt the coreos intercontainer network using flannel and tinc and vagrant. All relevant scripts and details are in the user-data file (cloud-config).
For more information on tinc-vpn see http://tinc-vpn.org/ For more information on how to setup coreos vagrant please refer to the orignal coreos vagrant documentation https://coreos.com/os/docs/latest/booting-on-vagrant.html .
While playing around with it you might find the update_cloudconfig.sh script useful.
HTH