You don't need an LOD tool or polygon reduction. What you need is less CSG.
CSG is a perfectly valid way of building level geometry. Not perfect, certainly, but you can hammer out a lot of level geometry in a short amount of time.
You'll never manage a clean mesh with something that builds geometry through a boolean operation like CSG.
Hence the need for a cleanup tool.
Building the model prefabs in a polygonal modelling tool, may be a better option in the future, I agree. I need to clean up the geometry for some existing Maplet meshes, though.
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I'm not sure if a polygon reduction/LOD tool would be the best choice. I guess it depends on the algorithm used. I don't want to change the shape of the mesh in any way, just rebuild the fractured polygonal geometry so that it is less fractured.