At the moment MDG does not provide a package build environment for Windows. However, if you do a normal meteor publish from a Windown machine, the package will be for Windows (the build machine is your own OS in this case). From a Windows machine, you can if you need to, publish for linux and Mac.
Most time you do not need to be concerned about the architecture for your package (it’s probably all Javascript) and just doing a vanilla publish is sufficient. To quote the docs (my emphasis, below):
Sometimes packages may contain binary code specific to an architecture (for example, they may use an npm package). In that case, running publish will only upload the build to the architecture that you were using to publish it. You can use publish-for-arch to upload a build to a different architecture from a different machine.
I suspect this is due to slow upload speed. I tested publishing after limiting my upload speed and it resulted in the same issue. They might have reduced the timeout. BTW I’m using a linux system.