specs say interior dimensions are 7' 8" for a 40' container. That might be tight with the tubes hanging but sitting at my desk thinking about it I bet it will fit. Taking the tubes off only takes and hour or so. or at least it did on my Zodiac that bolts inside and out. similar to go back on. It's not the end of the world.
I would bet the government had fitting in a container as a spec for the boat though.
I was worried about trying to fit my Willard along the side of the house - fully inflated at 9 ft was too much. The widest point of the hull at the transom is about 64 inches. Add a couple of inches for tube fabric and I think you'd be ok.