Regardless where or what makes the delay it shouldn't be any longer than what the manual has, or at least close. I control the delay in sheet cam on my machine. If you are controlling the delay with Mach, sheetcam should be set at zero and Mach should have the correct pierce delay for a given plate thickness.
Typically the torch is set higher than cut height during the pierce. The torch comes down during the pierce and arch stabilization happens after the pierce during the lead in. I wouldn't think that it should be two seconds on any profile. Surely it won't be that across the board.....
You may have to edit the cut profiles to get the delay correct.... or you just have a better handle on it than I... Good posibility....
AJ