You might be able to control Cortana by changing your Default program settings. In the new upgrade to 10159, I told Cortana to play music and the Music App started up, so it does not have to be WMP. Probably the default app for music files on this install is the Music app, so it opens.
It could be some utilities will not work with Cortana.. Only time will tell, but Cortana is working much better in this latest build.