I was creating an ExtrudeGeometry, not ExtrudeBufferGeometry.
My algorithm is to first create an ExtrudeGeometry, assign skinIndices and skinWeights, then convert it to ExtrudeBufferGeometry.
I built it this way since it is easier to assign skinIndices and skinWeights for ExtrudeGeometry since it is indexed which makes it easier for me to track the vertex indices. As opposed to ExtrudeBufferGeometry which is non-indexed, which means the sequence of vertices in the position attribute is all over the place.