I have tried to find the sentence you quoted in the article and was not able to. But it is not true that "every large aircraft (...) carries an IFF". IFF is strictly military. What civilian aircraft do have (large and small) is a transponder. The article talks about this but in a confusing way.
Eh. Military aircraft would also have a transponder, they just wouldn't necessarily have active broadcasts.
Civilian aircraft do broadcast actively (ADS-B). But they also respond to secondary radar for Mode A/C, which are basically cases of IFF Mode III (okay, maybe not exact term, but the idea applies.) So it's still a challenge-response/IFF, just in this case always responding.
Military aircraft use different modes and presumably don't respond unless interrogated with an appropriate challenge, but the principles are the same.
