Ideas on document annotation ergonomics

Yes, something like that. The highlight tool in the Zotero note editor also has a button “add to note” right under the color picker. Zotero also mostly keeps the blocks in order, but it doesn’t work on single pages.

One issue that bothers me is mixed text with math, sometimes copying text with formulas leads to huge blocks of newlines interspersed with symbols. I suspect that this might be due to incorrect OCR layers. For text with lots of math, it means one has to copy a line of text, then copy the formula as a picture, then the next line of text etc. Mostly I just take a screenshot of the entire block, which defeats the purpose of editing the text.
I don’t know if there is a better solution to copy text as text but formulas as images.