The mind boggles at this so I had to download and read the microsoft marketplace agreement myself and the sections cited are indeed in there. An app can't be entirely or even partially covered by any license that requires ANY of:
Jan Wildeboer » Blog Archive » Microsoft: Absolutely NO (GPLv3-or-compat-licensed) Free Software for Windows Phone and Xbox Apps.
I'm utterly floored by this. I can only assume it is a bit of legal and public posturing that they will back away from. Or it may just be a way of preventing any competing toolchains from being used. I'm amazed.