Certbot documentation states:
Most users should use the operating system packages (see instructions at certbot.eff.org) or, as a fallback,
certbot-auto. You should only use Docker if you are sure you know what you are doing and have a good reason to do so.
What are good reasons to use Certbot in Docker?
Is it better to run Certbot inside my app container? Or is it better to run Cerbot in a separate container?
I (personally) don't suggest you to use certbot inside Docker.
Docker uses inconsistent storage, which won't save your files (certificates) after you detele it (unless you configure a external storage to store the certificate / key / account files).
For example, if you are using a staging or production container and plan to rebuild it quickly, you'll hit rate limit pretty fast and unable to issue any certificate after that point (up until the rate limit issue disappear).
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