A typical signal cabinet has a conflict monitor, also called a malfunction management unit, that’s physically distinct from the controller. It supervises the controller outputs and can force the signal to all-way flashing red if green (or yellow or WALK) is shown for conflicting phases or if red or DON’T WALK is missing. More sophisticated units can also detect problems with sequencing or change or clearance interval timing.
I think that interlock design also goes some way toward mitigating the security risks ASCT systems would otherwise pose, as mentioned in the article. On any decent controller, even the control room shouldn't be able to deliberately trigger conflicting phases.