1. C9 is not a place where Microsoft employees will give legal advice or get drawn into complicated discussions on policy.
2. Emails can, and routinely are fabricated to look like they come from the wrong place. Just because it claims to be from the Windows Store team doesn't mean you should click links in the email and type in your password.
3. The word "may" is important in the second paragraph. It is not "will".
4. The best place to get feedback on this is probably via the developer support on the page where you submit your app to the app-store. That will allow you to contact a representative at Microsoft who can deal with your request/complaint specifically, confidentially and authoritatively.
5. if Microsoft claim you are breaking a policy of theirs, Microsoft's word is final. If however they are claiming that you are doing something illegal and you disagree with them, Microsoft's word is not final. In that case, consult an attorney.