You are absolutely right. And deployment can be set up to open up additional vulnerabilities and holes. But there are also many ways to make the deployment quite robust (e.g. upload via push to a deploy server, distribute from there). ... and just by chance, I've written a small bash script that helps to distribute SSL certificates from a centrally managed "deploy" server 8) [1].
[1]: https://github.com/Sieboldianus/ssl_get