On the regular GI aperture, the large aperture is 2 MOA lower than the small one. That means if you zero the small aperture at 25/300m, the large one will be zeroed at 50/200m.
With a same plane aperture, the big and small apertures are the same height, and so they will both be zeroed at the same distance. Whether it is an advantage or a disadvantage depends on the use.
If your use simply requires hits on man-sized targets at typical engagement ranges, the GI setup is probably preferable since it allows you to quickly switch between your near and far zeroes depending on the situation, and since you probably wouldn't want to use the small aperture at close range anyway.
For competition shooting, where you might have to shoot a match that has a stage with a little bit of precision shooting and a little bit of speed shooting, all at close range, you might want to be able to flip apertures in the middle of a stage, all while keeping the same zero. Also, you will generally know the layout of a stage before you shoot it, so you will be able to set your zero beforehand based on what the stage requires.