Yes, I don't think Certbot is very well-optimized for that. For example, there's no option to request a certificate to be saved in the current working directory, except with --csr, so you can't do that if you don't have or don't want to use a CSR file.
Certbot is most optimized around doing its own automated renewals with its own web server integrations or with mostly-Certbot-provided authenticators and plugins that handle certain other cases well.