Skimming from the dozens of pages I would love to have read back then, I think this may be the case of writers creating a detailed setting for the game early on - only fraction of it could become part of the gameplay, but presumably designers and writers were using it as a reference. And, come release time, it didn't hurt to include the world-building bits - it might just get some players to enjoy the game more (I know it would've had this effect on me), while the alternative, back then, was for those details to never see the light of day.
And/or maybe they hoped to make some follow-up games, or tie-in novels, etc. - then including those details was both important to solidify the fictional universe, and would drive some secondary sales for the game itself.
More interesting in retrospect, the first manual contained extensive descriptions of kiith clans. They go on for dozens of pages, and don't show up in the game at all. Someone spent serious effort writing them. Why? Left over from an earlier version of the game pitch where the player would have to manage relations between competing groups on the mothership? https://sierrachest.com/gfx/games/Homeworld/box/manual.pdf