As a mentioned over Twitter:
1) The Escape Pod is always the Last card, and since it is an Objective card, it doesn't go back to the deck if you can fullfil the win condition.
2) Indeed. This is here in case one doen't fing any Healing and end up with a Gear. It would be frustrating to not get any points for that, even though the Gear is useful. Maybe 5pts per Gear would make that trade more interesting.
PS: Let's try not subtract the total number of Threat cards, only the highest Threat power. By my experience, it's usually 7-10, that should be enough.