I tried Bear, but was frustrated by its tagging model. I want the tags to be metadata, to sit outside of the text content itself, but instead it makes you bury its primary organization system into your documents, leaving you to figure out either how to push them out of sight or how to make it seem like you meant to mention a tag deliberately.

The other gap: There's no way to refer to a tag (as a hyperlink) without making the current document "belong to" that tag you mention. You can't "point at" another tag, to express, "See tag XXX for more on that subject."

Were Bear to fix those two problems—and I concede that calling the problems as opposed to firm design choices is an opinion—I would consider using it.