Really it depends on what you're doing, in many cases I prefer the current results so I can pick which thing I was actually searching for.
But yes if you are editing code around all instances of a thing, highlighting works better as you don't have to start the search over to find each thing.
Obviously bookmarking the results is the proper thing to do. but it can conflict with other bookmarks.
Highlighting would have to allow jumping place to place, so you don't miss any.
Maybe to make coding it simpler for Ashley, and cover the bases, have a button to add "Search bookmarks" to the results. so after you clear the search filter you would have all the results in you bookmark window with orange flags instead of red.