If the INS is in AUTO it will go from 1 to 2 then from 2 to 3.
If you select 'Waypoint Change' '1' '3' 'Enter' it will take up a track from 1 to 3 completely missing out 2.
If you select 'Waypoint Change' '0' '3' 'Enter' it will go direct from present position to waypoint 3.
In the first case, which is what you are probably talking about, it doesn't actually go right over the top of waypoint 2 unless it is on track. If there's a turn it cuts the corner and passes 'close to' the waypoint rather than overflying it, then shooting out the other side and having to make a large correction back to track.
In the case of the positions you have given the turn is so small that there's not much of a corner to cut and it will pass very close indeed to waypoint 2, certainly within 400 yards.
Its an odd question. Is it a progress test?