[TaskManager] Determine if herd initialization needs to occur in `handle_single_simualtion_run()` if `simulate_animals` is false

[ew3361zh]

In TaskManager.handle_single_simulation_run(), TaskManager is triggered to handle_herd_initialization regardless of whether simulate_animals is True or False. This seems incorrect and once #2735 is complete, it should be easy to turn off if so. I think it's worth investigating further through testing and other means.