Maybe I'm getting something wrong here, but shouldn't rounding to 4 digits be more exact, than rounding to 3, thus eliminating the problem of matching the wrong vertices. As far as I know Blender supports 5 digits after the decimal point, where the smd format supports 6 digits. So it should be possible to round to 5 digits to get the closest match between Blender and smd.

In Line 892 in import_smd.py the coordinates for a vertex are rounded to three digits after the decimal point, which results in rounding errors for the vertex coordinates making it impossible for the import script to match some VTA vertices to the base mesh. I changed the the value from 3 to 4. Now all VTA vertices match the base mesh.