For new builds, its definitely due to the density of the wood, paint, and assorted hardware.
Remember, as "standard" as many wagons were, there was always variation. Rather easy to forget such variation can naturally occur in our world of computerized mass production.
Even in my line of work, our products often vary in weight by a pound or two, and they only weigh sub 100lb! Once you scale that up to a few tons, its not hard to see the range that's possible.