A sefer has a cover that when the cover of the sefer is standing upright the contents of the sefer are upside down. Which way would be the correct way to keep the sefer. It may be כבוד הספר to store it with the cover standing upright for then it looks respectful.
See שלחן ערוך אורח חיים סימן כ"ח סעיף ב' where you see that some keep their תפילין של יד on top of the של ראש and still we keep the תפילין bag upright although through that the של יד lays on the של ראש all day perhaps because the bag is in its right position.