Damage Markers can be placed on any Section of an Outfit
An outfit is made up of sections of two types; use spaces and empty spaces for storing cargo i.e. A use space is considered to be a section of an outfit. Therefore this rule
Damage Markers on an Outfit cause that Outfit to become less effective. Each (damage marker) placed on an Outfit ...
The swamp rat's ability allows it to place a damage marker on an outfit instead of an armed marker to perform an action but only when that action is valid. The engine cannot be used to make a move action when defending against an attack. Therefore you cannot use the swamp rat's ability to move to escape combat. You could, however, use it to power the shields ...
You cannot store cargo on the unused spaces of an outfit. The unused spaces are there to add complexity to the placement of your outfits and to also have a place for you to put damage on an outfit without it being disabled
Yes, you can win by purchasing a ship (upgrade to a higher tier). As you stated, the only method of gaining points that you are forbidden to use to win the game is buying 1 point for 5,000 credits. Other than that, anything goes