If the counterfeiters were worried about being sued for their practices they might have changed the board layout and some of the pin connections but I doubt that is the case.
This just reminded me of an experience we had with some of our first IBM PC clones. It's been almost 30 years so I don't remember all of the details but I do remember that we started out with two genuine IBM PC XTs and we expanded with clones that we assembled ourselves. The motherboards looked identical but we had one program involving the timer and/or speaker that worked on the genuine IBMs but not on the clones. We eventually found one PC trace that was broken or missing on the clone board. The boards were otherwise identical and it looks like the clones were manufactured on the same assembly line. The clones could have been a midnight project by some rogue employees or just a rip-off by the subcontractor.
By the way, we got into the clone construction mostly because of IBM's greed. Our PCs were purchased on 'state contract' and New York, in it's infinite wisdom, purchased the computers without any warranty. One of our hard drive controllers failed shortly after we got the machine and IBM wanted an outrageous price for a replacement. We found an ad in Computer Shopper for a controller and hard drive at a lower price than IBM wanted for the controller alone. When the parts arrived we found that the controller boards were absolutely identical. That's when we decided to build our own computers and we never did buy another genuine IBM machine. Things might have been different if the motherboard experience had preceded the hard drive experience.
Don