Fix namelist variables that weren't being set

[billsacks]

Description of changes

With my upcoming fix for ESMCI/cime#3984, I
was getting some failures due to namelist variables that weren't
properly defined.

(1) mediator_read_restart: since this is set in the code rather than via
the normal mechanism, I think it's appropriate to have
skip_default_entry="true" here.

(2) ESP's pio_netcdf_format: I'm not positive that the way I've set it
is correct, but it seems more correct than before.

Specific notes

Contributors other than yourself, if any: none

CMEPS Issues Fixed (include github issue #): none

Are changes expected to change answers?

• bit for bit
• different at roundoff level
• more substantial

Any User Interface Changes (namelist or namelist defaults changes)?

• Yes
• No

Testing performed if application target is CESM:(either UFS-S2S or CESM testing is required):

• (recommended) CIME_DRIVER=nuopc scripts_regression_tests.py
  • machines:
  • details (e.g. failed tests):
• (recommended) CESM testlist_drv.xml
  • machines and compilers:
  • details (e.g. failed tests):
• (optional) CESM prealpha test
  • cheyenne & izumi (all compilers)
  • details (e.g. failed tests): only test failures are ones that seem to have failed in the baseline, except for a couple of tests that looked like system issues. NLCOMPs identical except for the expected change in pio_netcdf_format for ESP
• (other) please described in detail: CESM's aux_cime_baselines
  • cheyenne (all compilers for which tests are defined)
  • details (e.g. failed tests): all pass; NLCOMPs identical except for the expected change in pio_netcdf_format for ESP

Testing performed if application target is UFS-coupled:

• (recommended) UFS-coupled testing
  • description:
  • details (e.g. failed tests):

Testing performed if application target is UFS-HAFS:

• (recommended) UFS-HAFS testing
  • description:
  • details (e.g. failed tests):

Hashes used for testing:

• CESM:
  • repository to check out: https://github.com/ESCOMP/CESM.git
  • cesm2_3_alpha03a, with the cime branch in Raise an error if no value can be found for a namelist variable ESMCI/cime#3988
• UFS-coupled, then umbrella repostiory to check out and associated hash:
  • repository to check out:
  • branch:
  • hash:
• UFS-HAFS, then umbrella repostiory to check out and associated hash:
  • repository to check out:
  • branch:
  • hash: