I am doing IPE too and come from China, though I did my undergrad and MA both at top-tier US colleges. I believe if you can produce a stellar MA thesis, at least from what I was told from my adviser (a leading scholar in IPE from Stanford), this will help a lot in top-20's admissions. I don't think Peking/Tsinghua's 3.5 would be a big negative, considering you lifted it up through a MA program. For Chinese foreign policy, why not consider programs like UCSD too?