It’s a non-starter for me because I sync my notes, and sometimes a subset of my notes, to multiple devices and multiple programs. For instance, I might use Obsidian, Vim and tasks.md to access the same repository, with all the documents synced between my desktop and server, and a subset synced to my phone. I also have various scripts to capture data from other sources and write it out as markdown files. Trying to sync all of this to a database that is then further synced around seems overly complicated to say the least, and would basically just be using Trillium as a file store, which I’ve already got.
I’ve also be burnt by various export/import systems either losing information or storing it in a incompatible way.
It depends what you want to do with it. If it’s just for storing files/backups then encrypt them before uploading and make sure the key never goes anywhere near the VPS. If it’s for serving up something like a simple website, you probably care more about data integrity than exfiltration, so make sure you have the security, including selinux or equivalent, locked down, and regularly run integrity checks. If it’s for running something interactive, or where data will be generated or downloaded to the machine, you’re out of luck, there’s no even theoretical way of securing that against an adversary with that much access.