I heard form a prof. at Carnegie Mellon of a Masters Student who wanted to continue on for his PhD, applied and was accepted to Berkley. So you definitely can go from one program to the other. The major drawback was that Berkley was only going to consider him as a first year graduate student so they would have had to do 5 more years at Berkley to get their PhD making a total of 7 yrs to get a PhD in Logic. As for getting in, I have no idea. I am sure your background will help and of course the LORs from professors in the field. What you could consider doing is applying to the PhD program, they admit some applicants to that program as Masters students (if you don't make the PhD cut). Then if you don't get the PhD you can go through with your plan.
