Just a quick note for CentOS 7 users: I pushed a certbot update yesterday so that you can choose the shorter chain via --preferred-chain. Currently the update is in epel-testing so you need to tell yum to use that repo explicitely.
The update will be available in the regular stable repo in two weeks. You can help getting it into stable by installing the update from epel-testing and leave positive karma there.
More details how to get the update via Fedora bodhi.