There’s an article that does a better job describing it written when the guy who ran the operation retired.
https://www.curbed.com/2021/04/al-putre-mta-money-room.html
Basically the money train was a dinosaur with operational issues. They moved to armored cars. My guess is that the transition reduced the number of station agents required and reduced shrink, but increased NYPD overtime. (MTA lost the transit police in the 90s)