The soundtrack features two Cut Songs, each of which originally had a purpose in the game:
"Federation" was to be the theme for the final sector, but it was not deemed climatic-sounding enough. Part of it was reworked into the new final sector theme, "Last Stand", making it a meta example of a Dark Reprise.
"Horror" would've been used for nebula sectors, but was found to be too scary, so it was omitted.
Originally, the game was going to have separate battle and exploration themes, but playtesting showed that battles only lasted 30 seconds on average. A new plan for the soundtrack would've involved a interactive soundtrack where every action adds to the music, but the composer Ben Prunty was opposed to that. After some negotation, the resulting compromise led to the "layered" sector themes in the final version.