There used to be 'illegal formation' penalties to attempt to control formations. However some folks shouted loudly, in the name of realism, that there should be freedom to use whatever formations they wanted.
So you now get these formations more. I actually don't mind either way since its a game but I'd guess that the original penalties were there to mitigate the unusual effects that can occur in an engine when people do unrealistic things.
(Sometimes when folks want realistic they get the unrealistic and even the surreal >.<)