It should be possible to set up several different types of communication over one USB. Each different type (HID, Serial) can identify itself separately. It must also be possible to do several items of the same type - I have a phone that shows up as 2 storage devices when it's plugged in.
Doing that through the Arduino libraries? I think it might take a lot of deep understanding how USB really works.
SerialUSB doesn't seem to be dependent on baud rate. You declare a baud rate in the SerialUSB.begin() but it doesn't seem to matter if the serial monitor names a different baud rate.
In the worst case, plug in a second USB on the programming port and use Serial.