Thank you @anon848905, you got me on the right track. No more wrong errors in this project.
As I had written, this is not about Scripture References in the technical sense. All we do, we mention in the Glossary, in prose, that people could eventually read more about Mr. XYZ in certain chapters.
So when you sent me to number settings, that did the trick. Since we follow the syntax of the Scripture Reference Settings, we would write 12—16 when we mean chapters. Normally one might write 12 — 16, but we want to help our readers with some consistency.
So PT, not seeing spaces, has (correctly) reported the longer dash in 12—16 as a medial punctuation.
I had not understood the error messages, because “all the stuff that goes with numbers” (like decimal points or plus or minus signs) was in my brain not classified as “punctuation”. Normally when I get punctuation errors, it means there is a first-ever use of a character somewhere in text, so I had forgotten that there are several places where PT collects data for valid characters.
All is well, thread can be closed (I have not yet found where to tick that). I give you one pink heart and say thank you.