I would assume it was to alert you to POI, Dangerous Crossing, etc. when used with GPS. But I don't have one. I am almost certain it says this in that part of the manual?
EDIT: Starting on page 121 of your manual it talks about the alert beep and volume. I assume the alert light will flash when one these are triggered.
If i had to guess i'd say it blinks when there is a fire tone out...thats how my pager works...a little red LED blinks when it gets tripped. (alert) I could be wrong though, i don't own one.
The ALERT LED will illuminate after a WX Alert, or Dangerous XING or Road, if you exceed speed limit setting for Dangerous XING or Road as you approach within 1/2 mile of GPS coordinates.