Out of curiosity, have you tries logseq or silverbullet.md? They both have capabilities to query your notes similar to Notion.

I've had this challenge with structuring notes-data for a while, but haven't found something that suits my workflow yet. I have on my list to experiment with a sqlite solution.

Not the user you've asked but I'm using Silverbullet and have been loving it, it ticks every box of what I was looking for:

• Self hosted
• Stores files in plain markdown text format
• You can edit those files externally and Silverbullet picks up the changes
• Allows customization and expansion easily
• Provides queries that allow you to extend markdown to pull data from other files
• These use an SQLite db to get these things to work fast, but if you delete them they get regenerated
• Can be easily synchronized with multiple nodes by using synching to sync the markdown files

I settled on obsidian with the built in sync. The data is as clean as it gets - its very agnostic to the editor as long as it adheres to the markdown standard (plus flavors). I'm aware that I'm creating a dependency on obsidians workflow and plugins, but the cost of switching is very low considering how I use my knowledge base (I could in work case scenario work with my files with standard Unix tools).

You are free to choose whatever tool that works for you, personally I don't want my notes to be held hostage by a single vendor.

The closest to Anytype is logseq, but silver bullet.md is also awesome. And if you choose another markdown editor, you could use rsync/git/syncthing to synchronize your files.

When it comes to note applications, there is no shortage of them. Just make a informed decision that will serve you well in the long term.