It will help to view the robot's collision geometry data instead of the visual data as they might be different. To do so,
show(robot, config, "Visuals", "off", "Collisions", "on");
You can also view the end-effector body's collision data by inspecting the Collisions property of the rigidBody
The next good step will be to find out which bodies are in collision. This can be done by viewing the separation distances between the bodies.
[isColliding, sepDist] = checkCollision(robot, config, "Exhaustive", "on");
In order to find out which bodies are colliding, you can view the entries in the sepDist matrix which are NaNs
[b1, b2] = find(isnan(sepDist));
Note that the rows and columns correspond to the body indices. The last row and column corresponds to the robot.Base body's collision with other bodies.
Adjacent bodies are ignored for collisions hence their separation distances are Inf.
Once you have found out which bodies are in collision, you can modify the collision data associated with that body to make the robot self-collision free for that configuration.