As if security weren’t hard enough, attaching a compromised Thunderbolt device can write the flash ROM on the computer. A system reinstall or drive replacement has no effect, since the EFI firmware is modified. You’d have to throw away the Mac—that is if you had any way of discovering the hack. This sort of thing is why high security users do things like glue USB3 ports shut and disconnect wireless and tape over cameras and so on. Certainly never, ever plug in a USB3 stick you find on the street (so to speak). Your good luck may be no accident.
This sort of hardware vector is unnerving, because there are all sorts of waypoints betwen the manufacturing of a device and its delivery. And no conventional way to detect the exploit. MPG has little doubt that the NSA has used such techniques to compromise systems, not that such activities need be confined to spy agencies.
Additionally, other Thunderbolt devices' Option ROMs are writable from code that runs during the early boot and the bootkit could write copies of itself to new Thunderbolt devices. The devices remain functional, which would allow a stealthy bootkit to spread across air-gap security perimeters through shared Thunderbolt devices.
More unnevering is that Apple would store a certificate in writeable flash memory, which can simply be overwritten. And that this bug has been known for two years and that it can be fixed, but has not been fixed.