For what it's worth, PDF Xchange Editor can do the following actions on any given set of search results: highlight, underline or strikeout all. They call it "Annotate Search Results", available as a free feature, though it can't automatically set a common "note" to all search results being annotated. Not sure if that will ever be possible, as they've yet to fix another issue where the option to copy the text being highlighted into the highlights' "notes" is
only executed when the user adds the highlight manually.
And of course it handles only PDF format.