There is an additional 15 seconds before you get a penalty brake application. The alerter begins sounding after the first 25 seconds, low at first, gradually getting louder. There is also a large red "Alerter" indication on the TOD (Train Operator's Display) that illuminates as soon as the alerter begins to sound.
The engineer does not see a counter. (There is an LED display showing the counter on the Alerter module of the ATC rack, but that is buried behind 2 separate cabinet doors and the fire extinguisher. )
There is a real time clock (with seconds) on the operating display of the CDP (Central Diagnostics Panel) that the engineer could monitor, if he wishes.
BTW, there was a 2 page article in Long Island Newsday (Tuesday, April 6) about the LIRR M-7s. If interested, check http://www.newsday.com
. You'll have to see if it's archived.