I’ve used letsencrypt, and there have been scattered successes on unraid, though I haven’t ever worked with it personally.
As far as the letsencrypt goes, there is a standalone mechanism that allows you to download a properly verified SSL (certbot-auto does it for me). In short, you should be able to get an issued SSL set of files entirely separate from MineOS. From there, we can adjust the MineOS config (/etc/mineos.conf) to utilize that SSL and it should work. Have you been able to get the cert downloaded from the standalone web server?