This is a manual version of what's meant to be an automated process. I believe the idea is that certificate revocation is a big mess right now, with Chrome not using the main revocation registry, and other browsers not being great at checking / enforcing revocations.

So the EFF decided that since automated certificate regeneration makes how often a cert expires irrelevant, they should use short-lived certificates so compromised certs can only be used maliciously for a short window, regardless of how well any given browser honors revocation registries.

I can't speak to whether this manual version of Let's Encrypt has flexibility in choosing certificate lifespans.