Multi material is fine until you want to light map, then it will be hit or miss. But yes having only a single material index makes it this way.
I am thinking the EBE stuff does this for materials, but not sure if it is from the floors only.
Material indexes on objects with more then one material have always had to choose the most prominent one you really wanted.
You can always split the model up into its material assigning each part the proper material index, but the majority will not do this and it is not a drop and run solution. I always split my models and then set them from a single point in the editor. For collision mostly, or if I actually need to tile out a material for a long ways.
So this would have to be done by splitting the model and having the correct material index set for each part right now, from a modeller perspective.
But this is my work flow for levels and not the normal for most.
Another way may be to assign the object some bones that you could detect the limb numbers and have the bullet hole chosen from there.
Again not a drop and run solution, but could happen this way with the current system you have in place already.
Let me play with an object that I do this to and set the material index for each one. I will post my results.
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