This is just the changed OpenSCAD, got to the original and give them the prusameters if you want the STLs and your brain can withstand disorganised hexagons.
The author remixed this model.
Holes are made as 2d geometry then the whole thing is extruded.
Holes are made in for loops using position arrays, god gave us vectorisation and thus parallelisation for a reason.
Aligned hex holes by rotating 30 degrees depending parity of for loop.
It's also a lot easier if you desire to change the hole numbers, just modify the positional arrays accordingly.