"higher binding energy" -- meaning that it's harder to pull them apart. Imagine you've got two pits, and you're moving bricks from one to the other. The deeper pit has higher binding energy -- it's tougher to pull the brick out of the pit, and place it into the shallower pit -- lower binding energy. The GP post is asking how this could result in a net gain of energy, when you've had to expend more work pulling bricks out of deep holes and placing them into shallow holes?
I don't know enough about chemistry to comment further, but that's my layman's understanding.
He didn't even do that, he combined two separate opensource engine making one better engine.
According to the allegations, he did not combine two open-source programs into a super-bot. They claim that the current version of his bot (Rybka) is a copy of Fruit, and an earlier version of his software was a copy of Crafty.
As you said, he closed-sourced them and claimed them as his own without giving attribution -- thereby breaking the software licenses of at least one of them (Fruit), which is GPL.
I tell them to turn to the study of mathematics, for it is only there that they might escape the lusts of the flesh. -- Thomas Mann, "The Magic Mountain"