In a retrospective post detailing the making of Chapters 3 & 4, director Toby Fox revealed that the layout of Chapter 3 underwent multiple revisions over the course of development. Fox initially started with eight different segments (four boards and four minigames) which then expanded to 17 with the inclusion of additional rooms and interludes. The final game would trim it down to 12, with the third envisioned board (which would've featured a "city" theme) being removed entirely due to it not working with the game's overall style. Vestigial remnants of this axed board remain in Spoiler:the Sword Route, where a stripped down version of it appears near the end of the Original Game. A cowboy-themed minigame also ended up removed, with the final game distilling it heavily to a shooting gallery. According to Fox, this fluctuating approach was due to him wanting to keep Chapter 3's pacing from getting bogged down while still retaining the original idea of it being a homage to the Mario Party series and the Strange Fortress stage in Gunstar Heroes.

The various changes made to Chapter 3's layout are reflected in unused content left behind in the game's data. Among other things, the game's code still contains assets from the full version of Board 3, early versions of other boards and rooms, and corresponding unused dialogue, music, and graphics. The latter categories include both early versions of material found in the final game and assets that were removed altogether.