i find that funny because most people go the cob route anyway and use other modeling programs besides max. the 70% of those collision problems come from excessive exporting/importing.
say sombody starts a model in truespace 4, they finish it right, then they hate the uv tools and export it to another program like blender and add uv data. or pass it on to another team member for the uv map. so now you got a ship in blender, uv mapped and good to go, but wait you need hierarchy, so you go back to truespace and import it and set up the hierarchy. but alas in the confusion of file format hopping, you lost your uv data. sad. so you send it back to blender for a re-uv map, thus loosing the hierarchy. after finally getting it back to cob format in a convertible state, you convert, get it into game and find that there are collision holes all over the place.
the best way to gain full control over what goes into your model is by doing the whole model start to finish in one program. your output is only as good as your input (and the code doing the conversion). in other words crap in, crap out. modeling formats are proprietary for the most part, they have several versions of those formats under the same extension, and the developers of various 3d packages really aren't obligated to supporting 3rd party formats anyway, so they half ass the effort of implementation. i do look forwart to seeing what format support gets added to pcs2, but i absolutely refuse to use a 3rd application between max and pcs2.