Yes. It is permitted to run MATLAB dual-booted on the same machine, as long as the hardware identification information matches. As Window's idea of a nice hardware MAC differs from Linux's, there is a possibility that you might need to use udev naming rules to nail down the same MAC address for both operating systems.
You do not need to use the same username on the different operating systems.
The most common cause of getting the error 9 on Linux in these kinds of circumstances, is having accidentally typed in root as the username when activating under linux. You need to go back through the activation process and ensure that the name you use is the same as whoami shows . (Running MATLAB under sudo root is not recommended.)