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I believe I have finally found the answer. I have installed gazebo_ros_pkgs from source and did catkin_make. This gazebo_ros_pkgs is a meta package but it still had tags other than build and executable. I believe the problem is with that package as it has solved when I updated my ubuntu to 18.04 from 16.04 and installed gazebo integrated ros melodic version.

Also the reason behind second error where gazebo was not able to spawn the entity for controller manager is because , there is inertial element for my root link and kdl does not support that. Despite seeing that warning, I did not think it can do much. Also I have made a type when loading a joint_state_controller.