Kinda funny to call the current 90 day certs "long lived". When Let's Encrypted started out more than 10 years ago most certs from major vendors had a 1 year life span. Let's Encrypt was (one of) the first to use drastically shorter life spans, hence all the ACME automation effort.
To someone like me with hobby-level serving needs, the 90 day certificate life is pretty inconvenient, despite having automation set up. I run a tiny VPS that hosts basic household stuff like e-mail and a few tiny web sites for people, and letsencrypt/certbot automation around certificate renewal is the only thing that I seem to need to regularly babysit and log in to manually run/fix. Everything else just hums along…
I've been running an LE client (official one, dehydrated, others) on various system for ~8 years, and the one time I had an issue with renewing was when (AIUI) the LE folks changed CDNs and so their responses were (slightly) different and dehydrated needed to be tweaked:
* https://community.letsencrypt.org/t/jws-has-no-anti-replay-n...
* https://github.com/dehydrated-io/dehydrated/commit/e4e712c03...
Other than that, never had an issue.