> How is this more secure than simply creating new certificates and replacing the old ones is the authorized_keys files?
It’s more convenient for me than updating authorized_keys. When I build a new machine, for example, I first generate a new SSH keypair on the machine. Then I copy the server and user public keys to the CA. Once I drop them in the right folder, certificates get generated automatically and served over HTTP. Then on the new machine I set up cronjobs to refresh the certificates every two weeks. I didn’t have to update authorized_keys on a dozen other machines, and I didn’t have to inspect any host fingerprints.
> If a host has been accessed by an attacker due to an exfiltrated key in the past it's tainted forever.
Yes, that’s obvious (although I did mention shell script in my previous comment—been a while since I thought this through). The scenario I imagined at the time was more like, did I ever copy my private key to an unencrypted flash drive, and then lose the flash drive? I never let private keys leave a machine anymore, but maybe I wasn’t so strict about that five years ago, and when did I generate my main SSH keypair? Was it four, five, six years ago? I no longer have to worry about such things. I could have just rotated my keys, but with short‐lived certificates I now get the benefits of key rotation without having to do any of the work.
Now I tie all my SSH keys to a WebAuthn key, which provides even more protection, because within the three‐week window that my certificates are valid, an attacker would have to also physically possess my Yubikey.