That is clearly what he was doing and it's alluded to in Jerry's statements after that season. He basically said Jason kept interfering and was effectively the play-called and it wasn't fair to Callahan, because it wasn't the type of offense he came from. It's clear Callahan was changing the approach of this offense and Garrett was trying to prevent it. And then Jerry, in order to reconcile the issue, in the off-season, got Linehan who coaches a similar offense as Garrett.
But this is also implicit admittance that Jerry tolerates the meddling of guys like Jason Garrett. So why complain that Jerry meddles with Jason, when Jason meddles with whoever is brought on to help this team, after Jason has shown he sucks at performing that particular job?
This was also the same season, after JG took the head-sets that you had Witten and Romo yelling at Garrett on the sidelines. I'm sure this was partly the reason Jerry actually removed Jason completely from the equation last year, because his star QB was having enough of it.
Look, we put up close to fifty points against Denver, primarily on Dez's drag route, a route which was clearly introduced by Callahan, not Garrett. A route that has once again disappeared from this playbook.