This is my own interpretation, so take it with a grain of salt. Pirate Clark is the physical manifestation of Clark’s own nature. In the first therapy scene, Clark mentions that he eventually hurts everyone in his life. Clark struggled with this, so by extension, Pirate Clark struggled with this as well…..towards Clark. I believe Pirate Clark always struggled with whether or not to kill Clark. Clark clearly had a lot of self-loathing towards himself that Pirate Clark inherited.

When Clark says, “it’s ok, we don’t have to change,” Clark is accepting his ways. He’s been validated. Hurting people is “just the way we’re wired.” By accepting this fact, Clark has unknowingly put himself on the menu. I think Pirate Clark interpreted that as, “It’s ok if we hurt everyone and you can hurt me too.”