I would guess they have injectors for the filling at the centers of those cells. A Voronoi edge is equidistant from the two points it bisects, so it kind of makes sense that this would happen naturally if the filling is injected at a constant rate.
I'd guess more likely that they are chocolate nozzles -- it seems more straightforward to me to produce a precise chocolate "cup", pour or place the filling inside of it, then pipe a chocolate "lid" onto the cup. Presumably the multiple nozzles of chocolate would help it to settle flatter faster.
Edit: there's a video on Facebook that covers the whole process in a minute. My hunch is partly right: the wrapper and chocolate cup are indeed completed first, then a circle of peanut butter is indeed placed in, then the thing is shaken to encourage that peanut butter to fill the space uniformly. However the chocolate "lid" is just plopped on as one wide dollop from a hose, and then blown out across the cup with compressed air: so the Voronoi cells probably come either from this blowing phase, or else the hose has some sort of "spreader" inside of it or so.
When rocks cool, crystals start to grow from multiple seeds because of thermal/chemical impurities. If the material is sufficiently homogenous in composition and temperature, then the crystals from different seeds will grow at the same rate. When they grow into each other, a boundary between different crystal domains will form. Crystal domains formed this way look like Voronoi cells.
The peanut butter cup looks like this because it's injected from several outlets with an approximately constant flow rate. Each injector outlet forms a Voronoi cell of peanut butter under it.
I know the former bit. I don't see how the latter obviously follows. You're basically saying it's related because it looks the same but it's clear from the picture it looks the same.
Imagine that the peanut butter is not poured from the top, rather coming from holes at the bottom of the cup. Initially there's a radially growing patch of peanut butter around each hole. When the peanut butter patches grow large enough, they touch, and form an approximately straight boundary (if the flow rate is equal for all outlets) like the boundary between crystal domains.
Of course, peanut butter is a fluid, so its dynamics are ultimately different from crystal growth, but at this scale, it produces a very similar phenomenon thanks to its high viscosity.
I actually wrote into the Reese's company to find out what that was happening to their giant cups, and got no reply unfortunately.