It makes sense. Luckily, for PCIe power cables that bit of sloppy building doesn't matter as all 3 of each set are tied together on the PCB where the sockets are soldered. In other words each set of 3 wires act same as one big fat one. What matters is that the colors of each set into the plugs is the same.

Nonetheless that shows some very poor training of the folks assembling the cables. Running the wires straight takes almost zero time and effort...