I do not see how you can say it is irrelevant. In the present circumstance, there is no mechanism to protect hardware from rogue or malicious code. This mechanism can restrict drivers to controlling only those devices that they are intended for and prevent other code from accessing them at all.
As to the USB but being a single tree in the hardware. This assumes that the designer would not make separate USB trees in order to take advantage of the different MMU style. It make sense if one assumes that any external device is at the mercy of the user anyway so that it should be controllable by user space code and that internal devices may be essential to normal operation. In fact, from a safety perspective, it may be desirable to have external devices be exclusively controlled by user space code. For example, many systems incorporate the internal cameras and microphones as internal USB devices. There is an ongoing problem with malicious code using these to spy on the user. A mechanism that locks these particular devices out without otherwise disabling the USB subsystem would be useful.
You can not assume that the new MMUs are irrelevant by considering past designs for which security was an after thought. These are new designs in which support for security mechanisms is being built into the hardware adding new opportunities that were not there before.