with most sims they use one file for the briefing map, another for the MFD map and then yet another file for the terrain - and all in different file formats! This method obviously exposes itself to inconsistencies
But you really want much more resolution for the briefing maps, and much
more for the terrain itself.
Years ago I did a lot of work with fng2k moving terrains between Gunship and EAW / Strike FIghters, he also imported terrains from M1 Tank Platoon.
Thats clearly a different format than the Commanche files, but looking at his website
might be useful, for tools and info.
I've written a few tools for terrain editing, don't know how useful they would be...