Re-enable var and fv3inc reference checks for select atm_jjob ctests

[RussTreadon-NOAA]

The reference checks for the following atm_jjob ctests are no longer executed

• atm_jjob_var
• atm_jjob_inc
• atm_jjob_ens_inc

PR #1999 appears to have inadvertently turned off the reference check for these ctests.

This issue is opened to document restoration of the reference check for these tests.