I think the topic is more about, "Why only that one? The SMB ground theme is used often too, but not nearly as much as the underground theme." Playing Galaxy again, I really noticed. The underground theme is used liberally, and the main theme is heard in the Toy time Galaxy, when you get one of those mushrooms that doubles your maximum health, and that's about it.
SM64 and NSMB are examples of how there are no problems with creating new main themes, but underground levels get the same-old-same-old. And I mean, it's fine, I like the main themes for those games (except the athletic version of NSMB's, I hate that one). But it would have been okay to have the main theme play in some of the levels, and not sped-up as it was in the Toy Time Galaxy and in Toadsworth's minigames in NSMB. It also would have been just fine to get a new underground theme for those games.