Her abilities and triggers are in some cases unique yes, but not in what they do. Unseen Manipulator is the only one that actually does something unique, the others are obeys, damage, discards, draw or deck manipulation. You can argue that she does these in very slightly different ways but the end results are not really very unique. Looking at the top of the fate deck when models activate nearby for example sounds very unique, but in practice its not any different to other "debuff when models activate nearby" auras. Its difficult to see what is different about her compared to say, Allison Dade, other than that Allison Dade does more damage and is generally more consistent in the use of her abilities.
I don't think every master is super unique, obviously damage masters all do "damage" but Youko is just even less unique than the average master. The only other case i can think of this bad is Basse/Mad Dog Brackett in terms of "henchmen do the job better than the master".