Here's strip 99 of Dude in Distress, and another round of introductions. As I'm sure many of you already surmised after seeing the prison in the last strip of Episode 2, Black Ark Pen is another Con'qorian construct. Superior alien tech is just better at containing super-powered villains.
Now if he perceives himself as good and actually did help lil boy boom then I wonder how he justified that to himself, my best guess is something like "if there aren't enough villains she cant show how good she is".