The first picture I'm not sure.
The second one that the red arrow is pointing at that's by itself at the top and is white in color is the plug and play connector for the trailer brake controller. Just installed one of those this past Sunday. Very quick and easy.
This is the plug with the trailer brake controller connector plugged in.
This is the other end of that plug that wires to the brake controller then plugs into the above plug
The last picture of the connector on the bottom, doesn't have any wires going to it, its just a blank space on mine just like your's. Not sure what its for, someone with an SR-5 or Limited edition may know. I just have the Base model 2008 but all are the same connectors.