Tung,
If in the text you are transcribing there is no distinction in meaning between a superscripted and an unsuperscripted negative/minus sign, then I would indeed, as you say, use (substitute all) with the regular minus sign and mention that in the Transcriber’s Notes page.
In response to your second question, if you follow the as-yet-unpublished updates to the our Guidance (which Dorothy Worthington talked about in her recent NBA webinar, "Update to the Guidance for Transcription Using Nemeth Code within UEB Contexts. What Has Changed?"), then I believe you could follow the new item #6 under Additional Guidelines and not use Nemeth Code at all for "Point R", "Point T", etc, because they are single-letter names of geometric items.
Thank you for your, as always, astute questions.
–Kyle