That last version is named "The Sequel" in the sound gallery and it plays during the ending, the start of the goombella scene before the credits. Doesn't play when returning from keelhaul key.
I'm so in love with the fact that they lure you in with a more truthful remake of the Rogueport theme, to get you comfortable; just so that they can hit you with the UPGRADED VERSION RIGHT IN THE FACE MERE MINUTES LATER
i love the dynamic switch to different versions but i think i still overall prefer the original in terms of arrangement, (even though some parts of the new version are Really cool) orchestration, and mix