Game development is a complicated business, even if modern tools and engines do much to ease the burden and the level of tricky coding required. Nintendo, of course, utilises its own engines and techniques, meaning that there are a lot of coders in its shiny new development building and others besides busily doing some rather complicated work.
While insight into Nintendo's coding processes is relatively difficult to discern, the GameCube version of Pikmin's disc does actually have executable files for Windows; in other words, a debug version of the game is sitting in the code, ready to be run on a PC by those clever enough to figure it out. As noted by The Cutting Room Floor, once you're able to run the executable off the diminutive disc you're left with a buggy, rather unplayable version of the game. There are some tricks to improve matters, though the thrill is in seeing 'behind the scenes', with the linked page providing plenty of information on what can be found when running Pikmin on PC.
This is likely a remnant of Nintendo's development processes at the time, and an intriguing bit of information for fans of digging into hidden files and code. There's more to Pikmin than meets the eye.