The purpose of having this setting is to allow a user to change multiple but separate areas of identical flat color throughout the illustration with one click of the Paintbucket. For example, if you have a character who appears in multiple panels and you want to change the color of the eyes in every panel - this feature would allow you to click on one of the flat color fills of eyes and all of the other eyes of that exact same color would update instantly. Currently in Painter, to do this you would have to click individually on each "eye" to make the updates which is very time consuming.
This was my request. I need to add that this is imperative for doing comic book coloring where repeated items of the same color appear on the page. But it could also be helpful for those doing color illustrations with repeated elements of the same color or thumbnails with simple colors that repeats across the page.