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yes, the domain in the hosts file needs to be the fqdn. Let's encrypt will look for the auth file at the root of that. if you are already using this fqdn/webroot you'll need another cname.
I don't think I'm using the root for anything, just domain.com/.well-known/matrix/server. Would I be able to serve the challenge at domain.com/.well-known/acme-challenge/stringofcharacters?
I think so. letsencrypt will only be looking for the file that certbot creates, so as long as it can resolve the fqdn to your host and port 80 (http://yourdoma.in) is navigable, then you should be good.
certbot certonly --manual is what I need though I think cloudflare or something else is making it only resolve to https. I'm going to shelf this for now and come back to it later. Thanks for your help