My computer went crazy there and posted before I was through.
If you want to use a tn, you might say something like: in the following exercise, the highlighted digit in each number is shown in parentheses following the number.
Highlighted vocabulary words can be a challenge since we have only bold and italic. It would be possible to explain in a tn that vocabulary words are both boldface and italic to distinguish them from all other words which are either boldface or italic.
The BANA math committee is recommending that Guideline 5 (Font Attributes) not apply in a Nemeth transcription.
Since I don't have the whole book to look at, as you do, I couldn't say if I agree or not with your belief that the attributes of the headings are necessary. They do have "icons" with each heading so perhaps you could create icons that would accompany or replace those headings that occur throughout your book, explaining their meaning on the transcriber's notes page.
Please feel free to ask more questions about the use of font attributes. Nemeth Code is to be followed if that code addresses an issue, and it does address the issue of typeform indicators.