Yeah, self-transparency in WebGL is a very tricky thing. Especially when transparent objects overlap with themselves because the triangles don’t know if they’re in front or behind other triangles in the same object. Here’s a thread with a bunch of examples of odd behavior.
My favorite workaround is to try messing with setting depthWrite and depthTest to false, so it doesn’t check with the depth-buffer, it might help you get the result you want: https://threejs.org/docs/#api/en/materials/Material.depthTest