Other than the license and ecosystem, isn't the Windows kernel broadly superior?
If it were superior for containers, Windows containers wouldn't have withered on the vine.
.NET Core being truly cross-platform is pretty much an official acknowledgement by Microsoft that Windows is not the be-all and end-all. To use their words, they're "meeting developers where they live" instead of insisting that one size fits all, if that size is Windows.
Having worked with the Linux OS APIs and Win32 APIs, they both seem to have their advantages.