I'm entering the public policy PhD program at HKS in the fall, and my impression is that the internationally focused students outnumber the domestically focused students in most years. And a lot of people study development and/or have backgrounds working for JPAL/IPA prior to entering the program. PP is also easier to get into than PEG, so if you're interested in working with people at Harvard (professors in the poli sci and econ departments as well as those in HKS), I think it's a great idea to apply to that program. PP would also be a good fit for the OP given the program's more explicit bent towards policy. I'm also interested in development in Africa, and am pretty optimistic about being able to find people to work with. But it's probably true that most other public policy PhD programs are more domestically focused (and are probably even smaller), though I think PP as a concept is flexible and hybrid enough that you could probably study whatever you wanted to provided you had access to the right faculty.
I can't really comment on poli sci programs, but I just went through the whole process of applying to econ programs with a focus on development (and also seriously weighing getting a PhD vs. masters, and all of that other fun stuff), so let me know if you have any questions in that regard (and are interested in my vaguely more definitive opinions). Another thought regarding PEG is that you could probably construct your own PEG-like program at any other poli sci or econ program, so I wouldn't fixate on trying to get into a program with the words "political economy and government" explicitly built into its name.