Hi hi, a little! Raising the question resulted in changes being planned for the wording. These changes won't be in in time for launch and are a bit complicated to standardise but it's something we want to do.
However, I did get some tips on what they mean though. Atlas Passives only apply to maps on the Atlas unless they state otherwise. In most cases, "unique boss" means "map boss". The pinnacle bosses are in their own boss zones and the passives that affect them are specifically spelled out. If you encounter a unique monster on your way to the map's boss, it wouldn't be considered a 'unique boss'.
When a passive affects a specific unique monster, that's usually called out on the passive itself - like in the case of Breachlords, for example.