[r=x] doesn't create the region in a ball.

Setup:

1: Create a 3x3x3 cube out of command blocks with the command: /summon WitherSkull ~ ~ ~

{direction:[]}

and trigger the command blocks

2: Remove the command blocks and summon a WitherSkull with the name 'Origin' in the middle of that cube
/summon WitherSkull ~ ~ ~

{direction:[],CustomName:Origin,CustomNameVisible:true}

3: Hook up a command block with the command:
/execute @e[type=WitherSkull,name=Origin] ~ ~ ~ execute @e[type=WitherSkull,r=1] ~ ~ ~ summon FallingSand ~ ~ ~

Attached picture shows it aswell.