Wrong baking after Unwrapping.GenerateSecondaryUVSet()

I've met a problem with generating UV2 field for generated meshes using Unwrapping.GenerateSecondaryUVSet(). I thought this problem is somehow related to the way I've created these meshes, though it happens even for standard Unity objects.
Suppose we have these lighting setting

Spoiler: Settings

and settings for directional light

Spoiler: Directional light

Now for the lone object we have this code:

Code (CSharp):

1.     static public void GenerateSecUV()
2.     {
3.         var currentScene = EditorSceneManager.GetActiveScene ();
4.         Transform selection = Selection.GetTransforms (SelectionMode.Editable | SelectionMode.ExcludePrefab)[0];
5.         var meshF = selection.GetComponent<MeshFilter> ()ж
6.         Mesh mesh = mesh.sharedMesh;
7.         Unwrapping.GenerateSecondaryUVSet (mesh);
8.         EditorSceneManager.MarkSceneDirty(currentScene);
9.         EditorSceneManager.SaveScene (currentScene);
10.     }

Now let us have standard Unity cube, use beforementioned code, nake him static and bake with these parameters.

Spoiler: Result

Now we have some creepy thing. Looking at baked UV we can see this:

Spoiler: UVs

The same thing happen when I tried to bake my own generated object (sofa). It was like baking happened at the right places (where UV coords are) but with wrong light and not "complete".

I have new Unity 2017.1.1f1. I've had the same problem with Unity 5 and thought it's some bag of Unity. It seems it is not the case...

 

It is very dangerous to use

Unwrapping.GenerateSecondaryUVSet()

on generated meshes. It will change your mesh data, including uv, indices and even vertices!

You can compare the mesh data before and after calling

Unwrapping.GenerateSecondaryUVSet()

to inspect that.