In robotics, because there are so many different disciplines interacting, a good robotics program will recognize that different specialties are a good thing. If a department is full of only CS people, then it's going to have a real problem getting their robots to function effectively, for example.
You could contact the heads of the PhD programs at each department, and ask them how they see a mechatronics grad fit into their program, and ask what advice they have. I think taking this kind of initiative would look good for you, too.
