Nate, I didn't mean to leave your question unanswered. I still stand by my original suggestion, using UEB to show the diacritics and Nemeth only for the math symbols (equals sign in this case).
The examples from earlier posts that you found are good to compare the decision-making process regarding which code to use.
1. In the math word problem example from May 2019, (18 kazoos ...), a Spanish eñe occurs in the word piñata. A dot 4 was suggested here, which is a remnant of EBAE but surely works well in this new context and I see no reason not to fall back on this technique. A transcriber's note would explain this use of the dot 4 since Nemeth Code does not define this dot as an accent.
2. In the second example you pulled from July 2021 (geocentric), the use of math symbols in these pronunciations does not in itself make this a "math statement". However, we do not use UEB math symbols in a Nemeth transcription. Since the pronunciation method in this book example uses italics to show stress, transcribing them in Nemeth Code is not a problem to transcribe or to read. Since (46) is more commonly used in math as the Greek-letter indicator, and since (6, 3) is more commonly used as the single-word switch indicator, it might be helpful to mention in a transcriber's note that, within the pronunciations, (46) indicates an italicized word and (6, 3) terminates the italic typeform within an unspaced word.
3. The second example (March 30, 2021) is a nice clear example of using words in a math problem, using Nemeth throughout.
4. Regarding your project, the pronunciation markings provide important information concerning the topic at hand, which is how to pronounce a word. As with example 2, above, the use of math symbols in these pronunciations does not in itself make this a "math statement". However, Nemeth does not have symbols for diacritics. Transcribing diacritics and stress marks is covered thoroughly in UEB, Section 4 and in Braille Formats, Section 20.
I hope this clarifies the decisions made in these four distinctly different scenarios.