voxel-texture creates a MeshFaceMaterial with two materials:
this.material = new this.THREE.MeshFaceMaterial([
opaque,
transparent
]);
and uses the first if !isTransparent, second otherwise. They only differ in that transparent: true is set in the material parameters.
voxel-texture-shader always uses the first material, with transparent: false, so it cannot handle alpha transparency. However the vertex shader does include:
' if (gl_FragColor.a < 0.001) discard; // transparency',
for full transparency (glass), but it won't work for, e.g., water.
Should restore the secondary transparent material parameters.