I've done this and it works very well. I had a Digital Ocean droplet so used their DNS service for the challenge domain.
https://letsencrypt.org/docs/challenge-types/#dns-01-challen...
It also occurred to me that there's nothing(?) preventing you from concurrently having n valid certificates for a particular hostname, so you could just enroll distinct certificates for each host. Provided the validation could be handled somehow.
The other option would maybe be doing DNS-based validation from a single orchestrator and then pushing that result onto the entire fleet.
I use this to sync users between small, experimental cluster nodes.
Some notes I have taken: https://notes.bayindirh.io/notes/System+Administration/Synci...
> Get certificates for remote servers - The tokens used to provide validation of domain ownership, and the certificates themselves can be automatically copied to remote servers (via ssh, sftp or ftp for tokens). The script doesn't need to run on the server itself. This can be useful if you don't have access to run such scripts on the server itself, e.g. if it's a shared server.