I think that's because of the use of --csr. This command is rather "unique" and unfortunately the behaviour isn't (very well) documented. I wouldn't be surprised if certbot doesn't even generate a renewal configuration file when a certificate is issued with --csr. It would be very helpful if the behaviour of --csr would be documented properly.
One of the ways to "renew" certificates issued with the --csr command is to "re-issue" the certificate the same way as you issued it in the first place. I don't think certbot renew will be useful at all, as there isn't a configuration file in /etc/letsencrypt/renewal/ for those --csr certificates.