add check flags to GNU CI and fix for data_override ci failures

[rem1776]

Description
Adds the debug flags from the mkmf template to the gnu CI, now that all the tests should be passing with them. (draft cause this will need #1575 in first)

I also included an attempt to fix the issue below where a data_override test occasionally fails, hopefully the sync call gives it enough time for the file system to catch up with the test and not throw the netcdf error. I can't know for sure if it works cause it only happens like 1/100 runs.

Fixes #1480 (maybe.. 🤞)

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules
• New check tests, if applicable, are included
• make distcheck passes