Ok, so everyone knows...all it costs to make an app is a small yearly fee to be a "Windows Phone Developer" (iOS has the same type of fee). The OS "shouldn't" in any way effect a developer's ability to implement their security algorithm. If SE is willing to work with me or another developer it shouldn't take long to create a simple authenticator(Security Token) app, even Blizzard has an authenticator app for Windows Phone. I'm sure they could come up with some sort of NDA (non-disclosure-agreement) that a developer could sign so when square shares the required information regarding the security key the developer can't share it without getting sued.

Honestly we won't know there reasoning behind it unless they come out and say it...that being said I'm willing and I'm sure there are other devs out there who would take the time to make this app to help the Windows Phone community.