The flightstone/crest search will take the item in question, add it to your inventory, then try to find the best combination of gear that you own to maximize the value of that item. The score is the delta between your current Best in Bags solution and the best solution found that contains the new item.
If you have a case where you think a specific item is ranking too high or too low, follow the instructions in this post to create a snapshot ID and reply to this thread, we’ll take a closer look: