that would be a big assumption for him to make without SOME word from Shaun....that Shaun understood they were a package deal...
I think Shaun knew this from early on. He did say he couldn't picture Jeanne as a mum, basically saying that Zach is Cody's parent. He also said he admired what Zach did for what he did for Cody.
And he let Shaun know he thought of them as a package deal when he asked Zach to bring Cody to dinner instead of staying at home.
I think Zach's 'Will you help me' also referred to Cody even if at that point Shaun didn't know Jeanne was moving to Oregon. Zach told Shaun that he couldn't leave Cody before to go to Calarts but he won't pass the scholarship again. So he needs to figure out a way to do this.
I understand that at some point between the making up in the garden scene and the scene at the house with Jeanne, they would have had to talk about the future. Maybe putting that scene in would have broken the rhythm of the scenes. Like they had decided in the making up scene and now they were ready for action in the confrontation scene.
The last scene on the beach clearly showed that everything had worked out the way they wanted.