So the available tool chains might use iOS and macOS?
In principle it is a Optic Character Recognition problem (OCR).
GoodNotes on iOS has a OCR feature:
But you can see that it misses out words (even in this very clear font on the kindle).
It is even more strange because the “In this” is not in front of “chapter” but is put before the “However”!
PDFpen should be a tool that has a more advanced OCR.
But OCR might generate this kind problems in any app.
If you use a kindle, you might use the highlight feature and export the notes.
There was even a script to import it into Drafts somewhere here in the forum …
On macOS My knowledge is more limited but I know that ScanSnap Scanners come with a OCR application (I have to look it up).