Mr. King, you are venturing into exterior ballistics, which is a different critter. With rifles or pistols, the bullet will rise above the line of sight, and then drop below it. Where the two coincide will be the zero.
But handguns aren't normally fired that far, so it's perhaps a lesser issue.
The real problem, as you have correctly explained, is the position of the gun when the bullet exits the bore. And, as you correctly posited, the handgun is in the process of rolling up in recoil when the bullet exits the bore. Lighter bullets will get out sooner, and therefore hit lower, than heavier bullets that spend more time in the bore (all this presumes somewhat similar velocities).
Recoil operated semi autos (Browning tilting barrels) work because the departing bullet gives the slide and its parts a push with its recoil; the remaining energy ejects the spent cartridge, resets the hammer/striker, and chambers a new round.
And again, you are correct, there would be no reason for the gun to recoil if the bullet had already departed.
Handguns will also have a zero distance, depending on the location of the sights, the nature of the load, and the distance fired. If the shot is taken at longer distances, the 'exterior ballistics' thing matters, as it does in rifles.
But it is that 'gun rolling up in recoil' thing that also makes me wonder we ever hit anything with a handgun...besides the relatively light weight, single point of support, and short sight radius, how firmly we hold the handgun will also effect where it hits.
Moon