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

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. 