Where is the mod tool you refer to? Could you please give some links?
We can browse the structure of game data through RogueDat, yet did not figure out the format of level files.

I was referred to your community from MODDB: http://www.moddb.com/mods/star-wars-rogue-leader-3d The main source for Rogue Squadron 3D utilities is http://rogue.squadron.tripod.com/ It well may be that Xentax community also did some stuff in this direction, would be interested to hear from you.