The only thing that matters is having the correct file-path references in the blueprints. The folders and their names can be set up any way that makes sense to you.
It looks to me like Kuju intended for the "Default" folder to include all the basic elements of a particular type of rolling stock, then added separate folders for alternate versions. The alternate-version folders only have the files for things that are actually different for the particular variation. Everything else refers back to files under the Default folder.
Kuju could just as easily have named the folder "Common" or something else. In fact, along those same lines, the Common folder could be limited to just that: "bogie" XMLs, textures--anything that's "common" to all the variations. Then all of the variations, including the so-called "default" variation, could reside in separate folders of their own. For example...
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Freight
Boxcars
Common (truck blueprints)
Textures (trucks, wheels)
Railbox (railcar blueprint, IGS, numbering csv)
Textures (specific texture maps, numbers)
Conrail
MKT
etc.
This is just one way you could organize things, but as Marc said, you can put the whole lot in, say, the Boxcars folder if you wanted. The only caveat is the texture-file path references you used in your modeling program are coded in the IGS file. That means if, after exporting, you decide to move the ACE textures to a different folder you'll get file-not-found errors in the Blueprint Editor.