What that page in the Amiga History guide doesn't mention is that VillageTronic were responsible for initial distribution of OS3.1. If I remember correctly, the manuals even state that it's licenced to them for distribution.
I kinda doubt VillageTronic would have supported piracy...
I don't doubt that pirate copies leaked out, but the Commodore packaging from that page I'm 98% certain is completely legit.