Windows 10X64, GTX1080
Broken: 2.79 (+a)
Worked: previous version (2.76 ?)
The island_margin value seems to have no/minor effect in the new version of Blender when using a command line python script (to add a lightmap to meshes in a fbx file).
bpy.ops.uv.smart_project(angle_limit=66.0, island_margin=0.0, user_area_weight=0.0, use_aspect=True)
When importing the fbx in Unreal, compared to an earlier version of Blender, changing the value for island_margin from 0 to 1 has no to really minor effect.
Exact steps for others to reproduce the error
on the command line using a python script; open an fbx, add a 2nd uv channel, use the smart_project command from above, save as a new fbx file and open in a fbx viewer where you can see the uv layout.