I got my painted console from Bumperplugs, and those pieces below the console lid were not painted. In fact, when he sends you the console, those pieces are not even on the console that comes to you....you have to transfer the ones from your console to the painted one he sends you.
I personally never even noticed it until you mentioned it, and do not notice them being black in the car, as you never really look straight down at it. Up to you whether or not to paint it, as I don't think it makes much of a difference either way. In the pic below, you can see a small corner of the piece below the lid. As you can see, once the console is in the car, you can barely notice it because it is blocked by the seats, and I have that passenger seat moved all the way to the back too...
