Police say there are pegs on the bottom of the aircraft that indicate that a box was attached at some point.
This is confusing - first they say he was in the batter compartment, shown on your diagram, and then they reference an attached box.
http://www.9news.com/news/article.aspx?storyid=125161&catid=339
From CNN.com:
“At this point, we are thinking that he did not fall out of the balloon and is somewhere on the ground,” Larimer County Sheriff’s Office spokeswoman Eloise Campanella said. “The basket itself was not breached. It does not look like he fell out of it, but again, this is all conjecture.” Watch balloon land »
Campanella said authorities are searching the neighborhood for the boy.
“I’m very confident we will find him. I think it’s a matter of him being a little scared,” she said. “Maybe he’s not ready to be found.” Watch the balloon float thousands of feet over Colorado »
all there was on the bottom of the box was a metal rod about 12” long give or take coming out of the center. Being a weather balloon it was likely an antenna or lightning rod.