Quote From TreeofLife:
Your PhD offer will most likely be fine. It's just a formality at this stage, as long as there is nothing bad in your references. I'm pretty certain they didn't even check my references.
If I was in your position, I would accept the MSc offer just in case, and then decline it saying that you have got a funded PhD elsewhere when you get your offer letter. They will understand. I know this isn't entirely ethical, but sometimes you have to put yourself first.
Exactly this. If the PhD doesn't come through, there's always the MRes.
Ian