Try using this add-on instead of using the Destinations add-on:
https://www.esoui.com/downloads/info...Pins.html#info
Map Pins not only shows dungeon bosses, it shows the ones you have already killed IF you set your map filters to show both icons.
FYI, I suggest that you use either Destinations or Map Pins but not both because together they can use up a lot of your CPU cycles and they basically do the same things.