Those caps cover where the eyebolt that is in the toolkit can be inserted to allow the car to be pulled or secured. They have been on German cars for years. I don't know if those locations are used when the cars are on the ship or not.
Kyle, I agree that stickered Civics suck but disagree with your opinion on Nitrogen in tires. In addition to its slower overall pressure loss rate, it has a much lower pressure/temperature change rate. So when the temp drops to freezing the pressure drop in the tire will not be as much as with...
If the engine does not matter to you then I would tend towards the 2007, you might even be able to do better than the current offer. If there are other dealers nearby, see what they have available. They WANT to move the 2007's. It is true it is already a year old but you have to keep in mind...