Most of this stuff just affects chunk generation, not actual gameplay once it's been generated. Also, that sort of thing only has an effect from the server in multiplayer, since that's where everything is generated. Kind of like how the names files in AI War only have an effect on the host, not from the clients.
In terms of what a lot of those XML files do, it's pretty much about how exteriors, interiors, and undergrounds are populated with objects.
Lastly, it's actually 100% completely impossible to get a desync in this game because of the networking model. Same thing for any action game or FPS game or whatever -- desync has no meaning, because there is not a perfect sync to begin with, nor is a perfect sync required for play. It's pretty much just RTS games and the like (and some puzzle games or turn-based games, probably) that have the worry of desyncs at all.