If I had to guess the heter was meant to be a last resort when all else has already failed. If she’s alive and well there’s still a chance that she’ll come to her senses or they’ll reconcile.
Do you have any more information on the cases where Reb Moshe allowed Bachurim to sign a heter? I’m curious to know if it was cases where the wife refused to accept the gett or cases after the war where husbands couldn’t track down if their wives were still alive.