I agree. I'll put an issue into Asciidoctor core to rethink the TOC with respect to the embeddable HTML mode. Also, I think for the Brackets environment, it would be better to have an outline tree view instead of depending on the TOC in the document for navigation. I did something similar for Gedit, which you can see here:

https://plus.google.com/114112334290393746697/posts/Fk8v9K4ecc9