Well, usually there are two options of getting a residence permit (later you will need to apply for it in Germany): either as student (§16 AufenhG) or as researcher/employee (§18 AufenthG or §19a AufenthG (Blue Card)).
Option 1: If you are going to get a scholarship and be a student, the important point here is whether the English or German language certificate is required for the enrolment into the university. It indeed could be that the university will ask you to provide English certificate, however, for PhD it could be rather relaxed and depends more on your professor; if he wants to take you, usually he will be able to manage it even without English certificate, if he really really wants do deal with it (which is often not the case).
If you are enrolled into the university, or get a brief that you will be enrolled, I would suggest that it should be enough for the embassy.
Option 2: You will be researcher/employee. Then embassy will be mainly interested in your contract and size of salary, I doubt the language certificate matters in this case.