I haven't delved particularly deeply into all the related aspects, but it's my impression that some particular condition must be met before a crew will desert the plane. For instance, they will sit contentedly until a fuel leak drains the tanks, upon which will follow an immediate departure. It's not unlike the triggering of a bail-out.
The consequence of such a departing of the plane is its subsequent disappearance from the game and its counting as a loss (I strongly suspect--not fully certain.) The pilot/crew remaining aboard is related to the plane remaining as not a loss.
It might require some tricky code changes to have crew leave while the plane remains in existence.
Again, I don't have the full picture of what goes on here. Just a surface understanding of certain aspects as I look into such matters as RTB-ing or bailing out when certain damage is incurred.
But the existing PAL mod involving jumping into and out of planes/vehicles will already have dealt with at least part of the issue.