Dual Passport – Entry/Exit question?

Hi,
Im a Bangkok old-hand now living abroad with my Thai life companion and family. My son (born in Thailand) recently returned to Thailand on a NZ passport. While there he has secured a new Thai passport (his old one expired several years back, and wishes to stay beyond the ninety days of his NZ visa.
So my question is, having come in to Thailand on a NZ passport, can he now ignore this entry visa, and exit later on his new Thai passport? This seems to me to be fairly obvious, but my life companion says he will get in to trouble when departing Thailand since she believes the passports will be cross referenced.
Thank You for your input.