Replace "non-initialized" variable values with parameters

Currently several variables, including those that are auto-generated, are set to specific values when created to indicate that they have not been properly initialized, while still avoiding potentially random garbage values.

These values are all defined in their respective modules, but it would be better if instead they all used the same `unset_XXX` parameters located in the `runtime_obj` module. This would help clean-up the code, and provide a single location to control what these "non-initialized" values should be, at least for all of the host model routines outside of the dynamical core.