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I'm hoping it's just a false positive. I have everything setup to not be indexed, and I just signed up for the google search console (to submit an appeal) and the console confirmed this. I was using cloudflare to block "bots and scrapers" and that seems to have blocked Google's scraper/indexer. My best guess is they might have flagged it just for that, so I've turned it off for now.
As for security, it's an ever-evolving thing but I'm looking at ways to tighten it up. Since everything is behind Cloudflare, I also have them setting up SSL certs, and running firewalls. This lets me auto-ban "known malicious actors", as well as any IP's that aren't geo-located to the US. Server-side, it's not great though. I'm running unraid, which is... not known for it's security. Not sure if there is much I can do about that though until I re-architect everything on a proper server.
You should for sure move away from a proprietary OS. There are many ways to go about it. I personally use Arch minimal with hardened kernel. Everything runs in non-root docker containers. Commonly used distros are Ubuntu and Fedora. But there are many more to choose from. https://distrowatch.com/search.php?category=Server
Yeah, I used to run on proxmox and tried to roll-my-own stuff. I found it to be a lot of work in the areas I was less interested in, if that makes sense. I liked unraid for it's ease of use, although I think in the end the gameplan is still to eventually move docker/applications off of the unraid box and have it be only for storage. Then I can have a regular linux box for all my applications & vms.