Jonathon,
It'd be interesting to see if you get better results or at least more consistent performance after updating your code, let me know how it goes.
1) My estimate is that it gives better performance because the network can see further back in time. It seems like a good solution, to me at least, to give the network as much information as possible without overloading it. By implementing the frame skip so the network can see up to 12 frames ago I think you maximize the information to the network.
You mention performance, frame skip can have a HUGE impact on performance. Check out this paper
http://nn.cs.utexas.edu/downloads/papers/braylan.aaai15.pdf where they examine (to the extreme) the positive and negative effects of frame skip in the same 6 NIPS games. This paper does use evolutionary algorithms instead of DQN, but they beat the NIPS performance in a couple of games by having what would seem like a crippling amount of frame skip. Notice Figure 1 shows that Seaquest gets a large performance gain with 180 frame skip. That's 3 seconds of game time!
Islandman