The notes.html file (notes are stored in HTML format so they will work with WebBrain) is available in the thought Folder.
I tested editing a note outside TheBrain briefly as follows: Typed a line of text in the note (so it was created, I could have probably created it myself, but I'm lazy). Opened the Thought folder by clicking the + Tab and clicking Open Folder. Opened the Notes/notes.html file with BBEdit. Saved the note. The note didn't update in TheBrain, so I navigated away from the thought and then back. The note was updated. I didn't test synchronizing, again lazy. Someone who is more invested in this should take a bit more time testing it then me. I can't see this as being very popular because most people don't enjoy writing with HTML tags (or know how).
However, without knowing what the back-end sync and display code is doing, it SEEMS like is already possible right now with any/your favorite text editor, just without the single-click to open the .html document in the folder. /shrug