Coach Saban leads the assistants in the direction he wants them to go, just like the players.
Then there would be no point in paying to keep a guy around (like CKS) and you could plug almost anyone in and get the job done.
There is a reason we saw so many shake ups in the position coaches this year on defense, and it was because the defense didn't live up to the standard set by CNS. CKS didn't get fired or pushed out the door, because it isn't his responsibility (on a superficial level0 to have guys playing their assignments correctly. I mean it is, but it isn't...just follow me.
(The following is just from my knowledge of other programs whether hs/college/pro and what I have gathered from how our staff does things...it is my closest summation as to how it works.)
Position coaches work with guys in a small group basis. They know which guys are going to be most adept at performing their jobs on the field. So they make the recommendations to the coordinators based on what they know (concerning scheme/gameplan/etc..).
The DC/OC is in charge of implementing the gameplan for each game, or overall scheme of the unit (offense/defense). So after the coordinator puts in the gameplan, he'll be able to work with the position coach and see who ultimately works best for whatever is trying to be accomplished.
The HC (unless it is like Saban with the DB's) works with the DC/OC to formulate the gameplan for each game (or overall scheme/philosophy), and a way to implement it. He has to manage all of the Coaches the way a position coach would his players. If he can't trust his Coordinators to make the right decisions, then the team won't be successful. If the OC/DC can't trust the position coaches to have people prepared, certain units won't be successful.
Now, that being said...I am sure most HC will over ride someone if they feel they have to, but usually that does not breed success.