The Mesh.INSTANCEDMESH_SORT_TRANSPARENT property only works for InstancedMesh, not for thin instances.
For thin instances, you give an array of transformation matrices for each thin instance and the system simply use them “as is”. If you want to sort the thin instances, you will have to sort these transformations matrices and pass them to the engine through a box.thinInstanceSetBuffer("matrix", ...); call each frame.
An alternate way to make transparency work with thin instances is to use the new OIT setting in 5.0 (Transparent Rendering | Babylon.js Documentation):