Nice mods, I like what you did with the corners and the lights. Ultimately, I'd like to mod a couple of working lights in there, although I'm not sure using 88005 will be the route for me.
I suppose they did this to accent the drive shafts. Also, I think it gives the set a slight "model train" vibe, matching the colours to the rubber bands on the wheels. Personally, I've replaced them with black pins as well.