I don't know if it's common practice, but it wouldn't surprise me. There have been many stories of China immigration seizing one (ie, the Taiwan) passport if the traveler shows they have multiple passports. BR check-in staff at TPE and TSA have hinted to me in the past not to let China see, say, both US and Taiwan passports. So, it seems possible that they're using the lack of stamp as a clue that the traveler has a Taiwan passport.