Though I know the answer to this question, a player in my group was adamant for me to get a second opinion on this.
The other day a player in my group doing the final mission in our game decided to try and use move silently to by pass having to fight the Final Mission creature and win the game. I told him that by doing so he is not completing the mission which is to kill the creature if he is just sneaking past it. Since the card did not say anything about not working in final missions, he was stubborn to a fault in fighting me on this to win the game. I tried to explain to him that running from the final boss doesn't kill it and though he finally agreed to roll it out and won anyway he still continued to complain about it.
So my question is does move silently work to help you by pass a final boss fight? (which it should not since its an avoidance and not an instant kill.) My interpretation is that the final boss basically acts as a pseudo preliminary encounter creature, where if someone is to use move silently on it, a mission or final mission creature stays on the board.