Hi nightinggale,
Today, you cannot containerize a Windows app. You can only containerize Linux apps today.
And containers use the kernel of the Linux Host on which they run.
Once Microsoft enables containerization of their apps with a format that Docker can understand, then we will be able to run Windows Containers in Docker on Linux, like boot2docker. Licensing will come into play, in this situation as well, I think.
I hope this makes it clear for you. Cheers.
-Joe
P.S: There was another question similar to this for Mac OS - please visit Trying to Understand Docker on Macs for details.