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.