This is around-about way of saying that 90 days was a well-thought out duration to issue a cert and the process of renewing it manually is there as a positive (rather than passive) confirmation you retain control. These guys are doing a public service, on par with archive.org and the EFF. I'm not sure, but even though I've been using cron since before I was a teenager, I'm not throwing that entry in.
Edit: Whoops, so I was half-wrong, mea culpa. https://letsencrypt.org/2015/11/09/why-90-days.html Part 1 addresses the security issue I brought up, and part 2 endorses automation. My mistake.