OK, some actual numbers:
The paper is based on the centre section of an A320 fuselage. Assuming that corresponds to the production joins, it's 5.98 m in length. The O/D of the fuselage is 3.95 m. So, assuming a generous skin thickness of 1.6 mm, the total volume of material is approximately 0.118 cu m.
Assuming around 2,700 kg/cu m for aluminium alloy, that gives a total skin weight for the centre section of 320 kg. For the entire 36.6 m fuselage, skin weight would be around 2,000 kg (the figure in the paper is 2155.4 kg, so we won't argue with that).
So clearly the numbers quoted in the paper for "weight of windowless/traditional fuselage" are the skin weight.