To me, the moment when Peter makes him put his own tracker on in the episode is actually symbolic of Peter offering him a choice: Peter has never put his anklet on him, but this is the first time he's just left it there and walked away. Neal had the option to leave the anklet where it was and bolt; it was a sign of Peter's faith in his dominance over Neal that he knew Neal would put it on. :)

It'd be interesting to write a story where the tracker comes off for the last time and Neal gets a band tattoo'd around his ankle instead. :D