Clean up run_tower.py

In a discussion with @danicalombardozzi , Sam, and Gordon, we talked about a few items related to `run_neon.py` that would ideally be changed for clarification purposes. Rachel has run into a few confusing pieces of information while working with Danica, so we might want to keep her in the loop and/or tag her if she makes a GitHub account.

Here is our ideal tower refactoring wish list (for after `PLUMBER2` comes in):
- [ ] Clarify the use of base case. This is confusing for users because we use the same base case in multiple places.
- [ ] Start date is confusingly set to year 18 in `env_run.xml` based on NEON usually starting in 2018 and ad/postad starting on 0018 and 1018 respectively. This doesn't necessarily cause issues, but is confusing.
- [ ] AD spin up is set up with `--setup_only` but then requires `./case.setup` which could be misleading
- [ ] There is a duplication of code with `user_nl_clm` and changes in the first bit of the namelist are overwritten by the second instance of the namelist
- [ ] Use RUN_REFTOD instead of START_TOD in PLUMBER2 usermods & update buildnml `tod` accordingly