That goes all the way back to the original Cherry G80-1800 boards in the (iirc) late 80s. The idea is to get a more compact layout that preserves some of the advantages brought in by the IBM Model M to make it easier for your hands to find the arrows without looking down. Shifting them down a touch with the gaps to the left and right leaves that trait in place no matter where your hands are coming from.

There are “96%” boards that will keep everything tight-in. I have tried it both ways, and all else being equal I tend to prefer a gap, but some other tactile reference (I sometimes use a single dot of UV resin on the down arrow) will generally be good enough.