The only time we usually put it on a line on purpose is after a kickoff for change of possession. They should not be doing that when a first down is in question.
The other note you are talking about - the only job of the official under the goal in a 4 man (or 3 man) crew is to tell the referee whether the ball went under or over the goal post. That is what the official meant when he said he had the over/under. The referee (back by the kicker) decides whether it went through the uprights or not.