How do I respond to a review report provided as an annotated PDF?
As one of the people who writes reviews in the form of annotated PDF files + a summary review, I think I'm in a good position to answer this question :-)

At least in my case, annotations in the PDF are often of relatively small points. I expect you to address all points raised in annotations, but you don't have to prove it to me by mentioning them individually in your response. Many will be typos/grammar annotations, some about missing axis labels, etc. In your written response, just mention somewhere that all of the points raised in annotations in the PDF that are not specifically addressed in your response have been taken care of -- that's enough for me, and likely the editor.

That leaves maybe ten longer comments in the margins of the PDF. If you think that they are worth addressing individually, copy the text into your response and add your reply. That should be easy enough to do.