Genghis, There is, or will be, a course of the type you describe:
MSc Unmanned Vehicle Systems Design :: School of Engineering Sciences
The BMFA Heavy Lift Challenge you mention is certainly a very good project. The design optimisation part certainly does get the students thinking, but the detail design and construction is to a large extent dependent on having or finding people with the requisite model building and flying skills. Being able to screw together an Almost-Ready-To-Fly model is a long way from designing and building a serious contender for the heavy lift challenge.
I think it is fair to say that what the universities are doing is operating within the sphere of knowledge of their lecturers and lab technicians. If they have the knowledge they explore new designs, otherwise they take proven equipment and add their payload and flight control system. An awful lot can be learned about why a platform is not ideal that way, and then set about improving it.
Another factor is that a lot of the students doing UAV projects are not studying aeronautical engineering. They could be doing robotics, computer vision or software. The UAV is just a tool to achieve their project goal as much as their computer monitor or keyboard is.