So they are not actually measuring time. If you look at the actual article (which I linked in another comment), what they did is experimentally assign a number to the different states of their system just based on that state, but in such a way that these numbers naturally order the states. Then they did the math to predict how their system behaves using this number as if it were time, and those predictions match what they experimentally observed.
The point is that in this experiment the "time" is an emergent property of the system, and not something presumed. So this a stepping stone towards determining if the real time that we all experience is a similar emergent phenomenon, or at least helps other physicists investigate this possibility.
The "mini-universe" stuff is pop-sci BS.