With the document viewer, you can add graphical annotations to a viewed document and when you burn the document to PDF, those graphical annotations are included. However, if you use the comments feature on any graphical annotation, those comments do not get included in the burned PDF. Ideally, they would be included as a tooltip on the graphical annotation (or as a tooltip on special icon such as a light bulb icon or comment icon...doesn't matter). This way the burned PDF will contain the comments and they can be viewed as a tooltip on the graphical item but don't block any text on the document. Acrobat allows you to add comments to a PDF in this way. You just select the comment and click on the PDF and it puts a little comment icon there and opens a form to write your comments. The comments are hidden unless you mouse over the icon.
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