Inspired by "Gone Boy."
Bob never expected this to happen. Of all the mad and borderline implausible scenarios his deranged mind had cooked up, Bob never would have expected that he would end up hugging his longtime archenemy in an almost paternal fashion, without any desire to literally back-stab him.
Had Bob truly gone soft on the boy? Or was he simply tired of this repetitive cycle of attempting revenge and failing? Honestly, some of Bob's more recent attempts on Bart's life felt as though they had been done before. Perhaps Bob was just out of ideas. The last rational part of Bob's mind could have been subconsciously crying out for Bob to return to reality and stay there for good. Bob's last bit of humanity may have wanted to escape, the part of him that wanted to help children instead of harm them.
And, in a warped way, Bob was somewhat fond of Bart. Bob noticed how Bart could be clever at times, even when nearly everyone else underestimated the boy. Also, Bart and Bob did share a love of being the center of attention, and most other children wouldn't have even heard of HMS Pinafore, much less enthusiastically sang along to "I am the Captain of the Pinafore."
Whatever the reason for his mercy, Bob was fine with it. He would have to be content with his murderous fantasies remaining as fantasies.