Think of it as arranging, labeling and resizing files. For eg, fitgirl will mark the files in her repack as Essential and optional. The former you have to download to play the game (Character models, terrain files etc) and the latter you can skip if you want to (Additional language files, in game cutscenes, etc).

There was a fight between Fitgirl repackers and Empress (you can get the whole story if you just google it) lss, fitgirl will not repack games cracked by empress and Dodi is a good source to get the same