Does anyone know what the black square is inside center console next to the 12v outlet? (On 2009 SC430)

 

Mine (2005) does not have one. I wish it did because then you can run wires from your radio into you glove box.

My guess is that is what someone did on your car. However, it does look very "finished" so it might have come from the factory like that

 

its very easy to remove the heated seats controller and look directly at the back side of this gizmo too see what that is. Just pull the control panel up and slightly to the front, no tools needed.

 

On 2010 and later every other Lexus Model they added a mini-jack (3.5 mm) and a USB port for media playback.
I have looked in both the 2009 and 2010 SC Owner's Manuals but found no reference to what appears to be a
blanking panel for such a fixture.