You quoted it yourself: "to support our goal of furthering research in sleep and chronobiology." F.lux isn't just trying to sell an app. Also, Apple has a history of releasing user-friendly but very bare-bones, feature-light tools; f.lux presumably wants the option of releasing a richer app that does things Night Shift doesn't.
From what I understand, Night Shift does basically the same thing as f.lux. f.lux has been out for years, and I'm not aware of any particularly innovative changes done to it in that time.
You quoted it yourself: "to support our goal of furthering research in sleep and chronobiology." F.lux isn't just trying to sell an app. Also, Apple has a history of releasing user-friendly but very bare-bones, feature-light tools; f.lux presumably wants the option of releasing a richer app that does things Night Shift doesn't.