It doesn't change anything actually, but it adds empty dummy folders like the "Gfx" and "Sfx" (the previously unused folders). But in the Mod's "Data" folder, the structure is completely different than regular DA(or DL). There is a folder named "Ship Components", another "Political Parties", another "Ship Styles", etc. There is no "English" folder where the GC2Types.xml should (at least from my understanding) go. Is there something I'm missing? perhaps a patch somewhere that'll bring me up to speed?
It was this way in DL as well.
There is a folder for each type of thing you can mod; when you put an .xml file in the folders, the game will read it in and add it on to the base data of that type. The files in those folders can be named anything so long as they have the .xml extension. For example, my hull mod has a number of files in Data/ShipComponents so users can easily choose which parts of the mod they want to use--just delete the ones you don't want, and keep those you do.
If you place a modded file in the root Mods/ModName/Data folder, it will be used *instead* of the base file of that name, rather than in addition to it.
There is no localization in the mods folder (if someone wants to provide multiple language versions of a mod, they would just give each language its own mod folder), and thus no 'English' folder in it.
If any folders are missing from the expected structure, the game will make them. Thus the mystery dummy folders.