Garrett in the article essentially stated what I mentioned. Which is once there was someone in place he trusted he had no problem with letting go play calling.
I remember it the way you do. There was something going on with Callahan where Jason didn't want him calling the plays. Remember that weird press conference where JG was asked about Jerry making the play calling decision public early, and he indicated he wasn't happy about how the news came out. Then he was saying the next week that it didn't help the team to let that information out early.
Then there were the issues that season where Jason clearly didn't like some of what Callahan was doing, culminating in that GB game where everybody thought he was throwing Tony under the bus but where in retrospect it was probably a tiff between him and Callahan.
When he brought Linehan in, though, it was always with the expectation that Scott would be calling the plays, and I don't believe we've ever seen any evidence that it's ever been an issue. One, Linehan is a better play caller than Garrett was. Two, those two are very much on the same page offensively, and it shows.
As an aside, I do think there were probably some issues between what Tony wanted to do at the line and what Garrett wanted, too. It always seemed like there was an uneasy respect between those two for whatever reason.