As I noted elsewhere, Gibbs controlled the riffing capability Brunell had by telling him to throw the ball away should the play break down. The policy was security and predictability even though he had a QB with an ability for improvisation.
I have no idea what planes Shanahan seeks to control, but in my experience, control freaks tend not to be able to turn that on or off. And for some people it tends to become more pronounced as they get older, though I couldn't begin to tell you if that's the case with him. But he has shown a propensity for it in the past.
I would only note that he's new to this organization and these players, that he's the current alpha dog, and he's going to pee on everything to show that it belongs to him. My guess is that until these guys have proven themselves to him, micro-management of everything that he can have control over will be his default mode.
IMO, he will want plays run precisely his way, he will want the check downs to proceed as he designed them, and we will want to force that both as a learning tool and to create scheme memory in the players. At this point in the curve, repetition will be key. I find it hard to believe that riffing will be an option, at least at first.
I welcome any counter argument to that.