The hack for causing accidents by hacking traffic lights wouldn't work because they are physically incabable of giving green lights to the wrong combinations.
My understanding has it that it's a comparatively simple piece of hardware, and isn't networked. It certainly ever happens that they're wired up wrong, but aren't something you can remotely hack.
Well, this could help you detect malfunctioning/hacked unit. But I doubt it's installed on every traffic light.
AFAIK the traffic lights are controlled by PLCs which can be easily reprogrammed if you gain access to them.
On the other hand, I've had an assignment a few weeks ago to make a circuit to control some traffic lights for crosswalk, and I'm pretty sure it was simple enough that the only way to hack it was to have direct access to it with a soldering iron.
It's my understanding that it is quite specifically installed on every traffic light (in the sense that it's both the purpose of the device and that it's legally required). Note that this does not control the lights, it simply monitors and switches to flashing-yellow (until a manual reset) if there's an error.
It's explained under section "2.4 Malfunction Management Unit" from the study linked immediately under the Traffic Control Exploit of the article. Sorry if I sound like a curmudgeon, I don't know how else to put it.
I heard it during a talk at RSA a few years back. The explanation was that it is a physical switch, so only certain combinations can be green at the same time.
