If you save scene with method "EditorApplication.SaveScene(string, bool)", objects with "hideFlags.DontSave", still have their childs saved in scene (childs are not marked as "DontSave"). I know it is not really a bug, but I'm sure this can cause unexpected problems. Because I notice that childs are saved not with global transform coordinates, but with local, so in the saved scene they will have their primary position changed.

1. Open scene "Input".
2. Select game object "parent".
3. Click menu item "Test/Mark As DontSave And Save Scene", this method will set "hideFlags.DontSave" then will save the scene "Output".
and finally will mark selected object as "None".
4. Open scene "Output".
5. You should notice that game objects "parent" child is saved.

Reproduced: 5.0.0b21, 5.0.0b20, 5.0.0b10