The fragment shader needs to have the following macro (at the beginning of the function) to be able to sample the right shadowmap slice for the second eye :

UNITY_SETUP_STEREO_EYE_INDEX_POST_VERTEX(input);

(Documentation: https://docs.unity3d.com/Manual/SinglePassInstancing.html)
UNITY_INITIALIZE_VERTEX_OUTPUT_STEREO tells the GPU which eye in the texture array it should render to, based on the value of unity_StereoEyeIndex. This macro also transfers the value of unity_StereoEyeIndex from the vertex shader so that it will be accessible in the fragment shader only if UNITY_SETUP_STEREO_EYE_INDEX_POST_VERTEX is called in the fragment shader frag method.