For your 1st question, I think you are asking if you can commit a card to the mission that is not required for that mission? If so I don't see anything specifically prohibiting that. However I don't think that is allowed. I don't think I would allow it, but I could see someone doing so.
For your second question, I think you are confused by this
When the players complete 5 Missions, they are almost victorious!
The only step remaining is for the Enterprise to warp to safety.
• As soon as the 5th Mission is completed, players will no longer Draw New Threat Tokens or Reveal a New Mission
and skip those phases entirely for the remainder of the game.
• Play continues as normal, and the players now only need to Destroy all remaining Threats on the board.
• When 5 Missions are completed AND the last Threat on the board has been Destroyed, the players win the game!
This only happens when you complete 5 missions not after each mission.
Hope that helps.