When I had a cut-carry handle rear sight, I preferred running it one slot "back" from it's usual position to increase the amount of available rail space forward of the sight.
However, particularly with military rifles - the number one reason you will see carry handles mounted a slot back is that it needs to be mounted that way in order to fit into a USGI M12 rifle rack, because the thumbnut/attachment lug would interfere with the locking bar of the rack if the carry handle were mounted in the "proper" position, flush with the front of the upper receiver:
(see the two carbines to the right - no carry handles mounted, but you can see how they would interfere with the locking bar)
While some users go ahead and move the carry handle for returning it to the rack, and move it back for shooting, very often, shooters will either simply not notice, or decide that it's better to zero in place than to zero their rifle, then take it back to the arms room, remove the zeroed carry handle, move it back one notch, then have to re-tighten it in the forward position again the next time they take it out.
Whether or not various "GI" legends have grown up around "why" it's best to use the rifle with the carry handle mounted to the rear one notch - the real reason is very simple... it's a lot like that old "cutting the ends off the brisket" story.
~Augee