They can lay them out anyway they want to. Its up to the design team, Some spread the PCIe X16 slots out, claiming better cooling bewtween cards if you run SLI or CF. You only have so many slots, so spreading them out does block the slots inbetween if you do SLI or C/F.
Putting all of the PCIe X16 slots in a row does help, giving you access to the other slots but does make the cards run hotter in SLI or C/F.
So its a trade off on whatever you need.