set netcdf_output_at_levels default to true

[szy21]

Purpose

Even though the z coordinate in the netcdf output is not correct, I think this is more useful for debugging as we can see the data on the raw levels. I kept one with netcdf_output_at_levels: false in ci to make sure it works.

To-do

Content

---

• I have read and checked the items on the review checklist.

[akshaysridhar]

I think this is perhaps fine for the CI plots since the design intent is to use ClimaAnalysis to generate the correct warped surface levels as a post-processing step. cc @Sbozzolo

[Sbozzolo]

Tests passing, feel free to merge