I think it's clear that we need to do a better job of presenting the distinction that you make above to new Let's Encrypt users, especially to users on shared hosting whose prior experience or awareness involved paid CAs that commonly issued certificates valid for 2 years.
When Let's Encrypt started up, there were a number of users who were rather upset that Let's Encrypt didn't offer an ideal drop-in replacement for these paid CAs (for example, see the old "Pros and Cons of 90-Day Certificate Lifetime" thread). Let's Encrypt has consistently said that automation is necessary for reliability and scalability, but not necessarily communicated that well to every prospective new user (nor necessarily always communicated well whose responsibility that automation would be in a particular setting).
As I've mentioned recently, I have a colleague who's starting to study new users' experiences with Certbot, and I believe that will include new users' experiences with deciding how to apply Let's Encrypt to their sites more generally. I hope one result of that project will be a better experience and better guidance for people just starting out with all Let's Encrypt services.