I don't think this changes the way the second is defined. Rather, that definition describes some theoretical ideal where the cesium transitions are all perfectly equally spaced over the course of the second.
I think this new clock is simply able to generate more precisely spaced ticks than those of a traditional Cs clock. Less jitter and variation in the timing of those ticks. Similar to how a one-hour water clock or sand timer's runtime will vary between "transitions", but a one-hour quartz stopwatch timer is much more regular. I could keep going, but I'm already out on a limb so I'll stop before my own uncertainty rises too much.
(Edit: I read the article. I don't think my words above are correct.)
How can anything … you know what? Never mind. No matter what answer anyone provides, I won’t understand.