Yes, PlaneShift does indeed use variants of the file format. One point is using data files converted from a readable XML based format to a packed binary format (
docconv). Another point is the use of factories of mesh objects in rather complex worlds to efficiently store e.g. houses with the same design but different locations, while handling them also in different configuration files for dynamically generated items. And furthermore, former closely related files (mesh factories, textures) get separated by type and stored in different ZIP archives which are later logically re-united in the Virtual File System.
This whole concept may be too complex to be thoroughly discussed in a forum. Also it may not be the intention of the development team to support any kind of modification, especially not if it changes the game balance: The engine is public, but "the game" (consisting of audio-visual as well as logical game data) is copyrighted; if you want to "change the world", you will make "a different game".
The above mentioned may not exactly be the official opinion of the development team; but I hope I didn't miss it completely...