The ALTER setting is something new and normally wouldn't be needed in most cases.
When looking at the timing of two loran stations there are normally two locations that have the exact timing delay/distance. The first is the correct location, and the other would be on the other side of those stations (wrong). This would normally be 180 to the other side of the stations (typically on land), at same timing delay. The ALTER setting allows you to flip the location if you find the conversion process has you at that other (wrong) flipside location.
Concerning the correction offsets being applied when you store the waypoint; that is news to me. I will need to look into that. I suspect that is a software misunderstanding on the programmers part.