You can do this with MarginNote 3. It is the only app I have found that can do this and I searched the entire Internet exhaustively to find a cross platform app that fulfills this request. I too am trying to keep a library of resources that allow me to drill down into tagging the content of a PDF rather than a general tag for the entire document. When you tag an annotation in Marginnote 3 it will allow you to search for it and when selected automatically reopens the document it came from to the exact page the tagged annotation is on. Pretty cool!