It sounds like you are super critical about any potential security issues (because what else could it be, other than that it just works or it doesn't). If given

It sounds like you are super critical about any potential security issues (because what else could it be, other than that it just works or it doesn't). If given machine security is super important (oh it's running a web server..), then why not just run certbot elsewhere and sync the files in a manner that satisfies your security needs?