From reading the above thread, I gather there won't be any magic of having Linux apps running on windows without a VM (current docker setup on windows runs Linux in a VM), or Windows apps running on Linux.
So basically this announcement means there will be a new way of running Windows apps in containers on Windows servers.
So containers will have OS dependencies now? :S If that is the case, it kills one of the major advantages of containers. A container should be able to run on any container host without any needing any knowledge of the nature of the container host! That's literally how they sold Docker. You make a container on your workstation, you can copy and paste it anywhere and it'll run. That's the whole damn point!
Docker for Windows already does this. The trick is it virtualizes a very small Linux system behind the scenes, but it is entirely transparent to the user. The result though is you can run any container from the Docker registry on Windows.
It would make more sense for Microsoft to add Linux API support, or at least fast-path/low overhead mode to virtualizing Linux on Windows so that it can run any Docker container, but.. that's probably getting too friendly with Linux to happen. :)