In the Sburb and Sgrub logos what does the box with a part slightly removed represent?

Up to interpretation really. It seems like it coincides with the Session Leader, Karkat, John and Roxy, but then the Dancestor Session would break this having Latula rather than Meenah land on that square, unless the Alpha Session monitors are arranged differently. Some people also suspect it has to do with the way John gets unstuck from the story, and how Roxy goes back with him in the Retcon Quest, but that still leaves Karkat a bit to the side. The logo also shares the shape with the Treasure, and of course it’s also the gate you go through at the End to Claim your Ultimate Reward, so who knows how deep the rabbit hole goes with what it represents.