If I select text in a document that has an associated comment, copy and paste that selection elsewhere in the document, I get the text and a duplicate comment. This seems correct to me.
If however, I paste with Ctrl-Shift-V to “Paste and match style” the text of the comment is also pasted into the document. This does not seem correct to me.
Q1: is there a way to “paste and match style” that does not also paste any associated comment into the document (whether or not it still duplicates the comment is immaterial to me)
To answer your main question: use the Edit ▸ Copy Special ▸ Copy Without Comments and Footnotes menu command. It’s the copying the matters, since that is what builds the clipboard, not the pasting. Once it’s in the clipboard as plain-text (which is being used for Paste and Match Style) there is no way for anything to know what a comment is or is not. It’s just text at that point.
So yes, when copying text normally, it will indeed include all of the content you are copying, including inline annotations and comments. You can for example paste text with comments into a word processor. In keeping with that principle, the plain-text variant that is created into the pasteboard also includes comments, annotations and footnotes.
Now there are areas in which this needs to be improved, such as presenting footnotes in a plain-text friendly fashion (like you’d get if you compiled to TXT), and putting markers around things so you can easily see what is a note or not—but it will never be the expectation to strip out content that you copy from. This would create issues where if what you copied is primarily or entirely notation, for instance.
Thanks @AmberV OK, got it, Edit ▸ Copy Special ▸ Copy Without Comments and Footnotes – one question: can I assign a keyboard shortcut to that? (My pref would be Ctrl+Shift+C; if that’s already assigned I don’t mind losing it elsewhere because I’ve never used it.)
I looked at Options… Keyboard… under Edit but there is no Copy Special group listed. Am I in the right place for this?
The same reason for why there is no global customisation in general. It takes a heap of code to add each command, and increases maintenance for each one added. There is just sadly no good framework for this outside of a KDE environment (on Linux), and probably because of that. We keep gradually improving it based on demand, but lesser used commands like these are best to learn the accelerators for, I’ll be frank.