One problem with md5mesh format is that it does not store normal vectors, so the mesh needs to be smoothed after it is loaded. If the artist used some custom smoothing schemes when baking the normals, the renderer has no chance of getting the correct results. I guess that Doom 3 smoothes the meshes uniformly or uses some sort of fixed threshold smooth angle, which is then also used when baking the normal maps.
Note that at texture seams, there are degenerate vertices, which should have the same normal. To properly smooth the mesh, it is not sufficient to compare if two faces share the same vertex index, but you must actually compare the vertex positions, possibly with some threshold distance.