I would email and explain- your situation isn't that unusual, I didn't get my final MSc results until the following January, when I was already 4 months into my PhD, so it shouldn't be an issue. Just explain and perhaps offer to send a transcript of the marks you have to date, or a supporting letter from your MSc supervisor, who should be able to state that you are expected to be awarded your MSc whenever. My supervisor also put my expected MSc grade on a PhD application, as she knew a couple of months before me what I was going to be awarded- it just had to be moderated before it was official. Your sup might be able to do that for you too. Good luck! KB