If it was mine, I would test how it sits all loaded in the water with weight, if the corner is still against the tube, I would get a shorter box, if it is only the side of the box against the tube, I would be fine with it. If you are wanting to leave the box in for trailering the boat, get a different box.
Maybe try calling up the manufacturer to see what they say about returns, can they re-sell the box if you need a smaller one? Guessing they say no, but could ask.
Think of me what you will, I got a little space to fill.