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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. Is the combination of reference and shallow not matching your expectations on both platforms, or only on one?
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.