Thank you! That's what I meant. I thought the boxes and arrows were on the actual print page and now I see you added that to explain the meaning of the bullets.
Even though these look like bullets, the text identifies them as dots, and that should usage should be followed in braille. I would think of these as icons which the transcriber creates with a shape indicator, rather than bullets. You might want to label these yd for yellow dot, etc. Place them as in print, preceding the entry followed by a space. List the icons in special symbols. Transcribe the boxed material at the top of the page, right after main heading, so the reader will have that information. If the box is repeated on every print page, I would NOT repeat it in braille, unless the information in that box changes, which is unlikely.
Do not use the dots in guide words. Transcribe guide words as if the dots weren't there at all.