Julie,
Only the format rules that are already in place such as the blank lines concerning headings or boxes if in the TOC and separating front matter from body matter.
I am unable to see your example, but Braille Formats 2.10.7 states that any line without a page number must end at least 6 cells before the right margin and 2.10.2 does not allow you to place TOC entries on line 1 or line 25 of a braille page to avoid confusion with the print and braille page numbers. Although you can use line 25 if you are doing interpoint on the even-numbered (left-hand) page where the braille page number is suppressed.
If you follow the above rules, does that help the transcription look “less muddy”?
Connie