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I just confirmed that using a reference repository with my 3 GB repository makes the fetch portion of the checkout almost instantaneous on the Linux slave I'm using. I use reference repositories on Windows machines as well with a 7 GB repository at work, so I'm reasonably confident that reference repositories are honored on both Windows and Linux.
I configured a copy of that job to use shallow clone and it also completed the "git fetch" portion of the job very quickly. I see from your log that it was generated on Windows, yet the bug report says it was visible on both Windows and Linux.
Are you attempting to provide a syntax for the reference repository which will work on both Windows and Linux within the same job? I've not found such a syntax in any of my experiments.