windows has "FC" aka file comparison (old dos utility) built into its dos emulator
FC /? for a command list while in cmd
what's stopping you from using 1 folder w/ multiple "mod" folders for each server you're running
you can specify which directory tribes uses by adding +mod MODNAME to the shortcut target
and if you're referring to "exporting" files, you can export to any folder within tribes' root directory, /temp by default iirc