However, the Swift project CI is not based on GitHub's CI---its separate Windows machines coordinated by Jenkins. So it's possible that there's something different in the GitHub CI environment for Windows that's causing problems.
In addition to the issues you mention, I suspect part of the problem is that the github CI only makes available two CPU cores for CI in the free tier that most OSS projects use, whereas Apple is likely using much beefier Windows servers for your own CI. I always suspected that had a role to play in earlier reported Windows flakiness on github CI.
@dabrahams and @taylorswift, have you tried paying for the larger runners on github CI to see if that brings the error rate down? Obviously this would just be a workaround for any current performance issues, but it may tide you over until those Windows Swift bottlenecks are optimized to work on just two cores.