You may notice that there is a padding at the bottom of the popover when you do not add any buttons to it. You can decrease or remove this via CSS.

.inmplayer-remove-buttons .inmplayer-popover-buttons {
  display: none;

You can add this custom CSS via Sites > Site > Settings > Player Appearance > CSS tab within the Inline Manual Portal. Once this is added, you can apply this to selected steps by going through the Advanced Panel of the Authoring tool and insert inmplayer-remove-buttons on the Custom Class field.