With a startup, there's a very strong profit motivation. With blue sky research, you're just exploring and discovering and inventing, and doing that without a strict goal of profit leads to unexpected things that wouldn't easily be found in other settings.
Not just startups (though the focus might have shifted toward them in recent years, not sure). The Wikipedia article says that Fellows are funded to "drop out of school and pursue other work, which could involve scientific research, creating a startup, or working on a social movement".