You’re mostly correct. The fees were implemented in 1993 for all transactions. It was part of a Federal government wide initiative begun in the 80s to charge users for services provided.
Shortly after, the Coast Guard eliminated the requirement to have a commitment of employment to obtain a Z-Card/MMC, the primary reason being the belief that the new user fees would deter persons from seeking a Z-Card who would not use it. See July 5, 1994 Federal Register.