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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