The upgrade finder finds upgrades relative to your current Best in Bag gear. It answers the question: if I swapped out my current item for this one, how would the score change? It is an estimate for how good the item will be.
It is possible (but rare) that you could get an item listed as an upgrade in the upgrade finder and then Best in Bag doesn’t suggest you put it on right away. There are limitations to how much we can calculate at once, unfortunately 
Best in Slot doesn’t care about your current gear - it looks for a solution from all the gear you allow it to consider.
The legendary search in the upgrade finder is slightly different than the rest. We have a post explaining it here: