Thank you for following up on this topic. Here is my long answer.
It is not a requirement for the reference symbol to be in the same code as its reference point. Depending on how you format this table, Nemeth may not be continuing after the referenced material. (That is how I was imagining it when I looked at the print.) I do agree with you, though, that it would be rather bulky to switch out of Nemeth, enter a UEB symbol, and switch back into Nemeth simply to avoid devising a symbol for the reference marker. However, in this case, you will not need to devise a symbol. Nemeth symbols already exist for the two in question (the section sign and the double bar).
The point being made in Rule 9 about UEB reference symbols not being used means UEB symbols cannot be used inside the switches. This applies to any braille construction, not just reference symbols. (A noted exception is icons.) There are other scenarios when one must terminate Nemeth in order to braille a UEB symbol, then switch back into Nemeth to continue; so this practice is allowed if that is your preference.
You will notice that the four reference symbols listed in Rule 9 of the Nemeth code (asterisk, single dagger, double dagger, and star) are the same exact constructions as their operation sign counterparts in Rule 20. These are not new symbols, they are just listed as possible reference signs. There is no reason you cannot go ahead and use the Nemeth section symbol and the Nemeth double bar symbol as reference symbols even though they are not listed as such in Rule 9.* Use (1256, 1256) for the double bar. (Dots 4, 6 do not hold special meaning.) Follow the spacing rules for symbols of reference which are stated in NC 9.3.
Since the section symbol and double bar symbol are existing Nemeth symbols, there is no need to explain their usage in a transcriber’s note unless you feel it would be helpful for the reader to be prepared that they do not hold mathematical meaning in this case.
As you noted in the last paragraph of NC 9.1, if you are using the Nemeth symbol in the text, you must also use the Nemeth symbol in the note itself. This may require the addition of code switch indicators depending on what precedes and follows the reference symbol in the note.
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* I thought it would be funny to include a footnote to my commentary. The paragraph sign and the section signs as reference markers were removed from the updated code book because it was thought that this usage was obsolete. It looks like you have found an exception! I’m wondering what the copyright date is on this material?