The debug stub will also work over a serial line, but debugging a usb device is a problem. If you use windows as host you can get a bluescreen by stopping the usb device. The enumeration is critical. I have seen Vista pass away by setting a breakpoint...
I have no experience about the behavior of the win7 usb stack.
What do you mean about the transistor stress ? The "mbed chip" usb and the mbed itself need two different USB ports on your PC ! Two cables.
It is possible to make a USB endpoint with more than one function : Composite Device. This device has more than one interface with descriptors for this functions (e.g. HID + CDC). The functions itself are working with different endpoints. One cable. It is tricky to get it working.
What you think:) Cortex-M0