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You can specify your physics engine in empty_world.launch:

You can do this by adding <arg name="physics" value="your_preferred_physics_engine" /> in Inverted_pendulum_world.launch, like so:

  <!-- We resume the logic in empty_world.launch -->
  <include file="$(find gazebo_ros)/launch/empty_world.launch">
    <arg name="physics" value="your_preferred_physics_engine" />  <!-- this line added -->
    <arg name="debug" value="$(arg debug)" />
    <arg name="gui" value="$(arg gui)" />
    <arg name="paused" value="$(arg paused)"/>
    <arg name="use_sim_time" value="$(arg use_sim_time)"/>
    <arg name="headless" value="$(arg headless)"/>

If that isn't sufficient, or you need to do more detailed tailoring of the physics, you could make a copy of (in which physics properties are specified), and pass that into empty_world.launch instead.