Whichever argument is correct (Rashi does not come down on either side though Ramban agrees that the Torah was within the Ark) the verse implies that there was already something in the Ark, i.e. the Decalogue, and this verse seems to be the source of the now universal custom that in the synagogue building the Torah scrolls (standing upright) are kept in the Ark whilst an artistic depiction of the two tablets of the Decalogue tops the Ark or is affixed nearby.
The original Ark was not a vertical cupboard but a movable horizontal chest sometimes kept in an adjoining room, and the Torah scrolls were stored there lying down. The vertical Ark seems to have been introduced in the period of the Middle Ages. In some makeshift synagogues a wardrobe was borrowed for the purpose of an Ark.