My experimenting shows that the embarked group is still located where they embarked, just invisible, for lack of a better explanation. So any trigger which relies on them leaving that zone will only trigger when they disembark the vehicle outside of that zone.
It's a weird implementation that I wish DCS would change. It would be ideal to make the embarked group follow the vehicle in which they embarked. E.g., once troops picked up in a helo have left the AO, a message could be given.
The current scheme makes things awkward.