Yep, that’s the only thing that was preventing me from doing a ./discourse-setup on the new server and then restore from the S3 image (and how to do this without access to the web admin console since the DNS would still be pointing to the old server and AFAIK discourse won’t response to a IP address in the browser). Since I had a live system and I needed to switch the DNS on the fly from the old to the new system, the lack of Lets Encrypt certificates was the only roadblock for me.
If there’s a way to transfer the certs from the old system to the new system, complete ./discourse-setup without any lets encrypt errors and restore from the S3 backup without the web console then that would be a simpler way to do this.