That’s how I read it too. More that they’re encoding another aspect into their pulsing. But “multidimensional time atoms” is probably a much more appealing headline.
Yep, this is it. The key is not that there are two time dimensions but two independent time translation symmetries, each which translates the system by a different period of time corresponding to the two frequencies in their pulse. The two time dimensions is an analogy that’s useful for the theoretical treatment of such a system.