https://www.youtube.com/watch?v=X2KA4eiqFII
Tree thing is clothed in orange, like Vincent Law.
0:45 fills up the empty syrup bottle with his finger, like Vincent fills the empty books with material and creates the scenarios they encounter. Or Jesus turning water to wine. "I think, therefore, you are."

0:49 father is working on the model spaceship. "The challenger"

1:06 rooster statues etc. They're framed between dog and rooster.

1:32 Playing the piano together. The character Pino plays the piano (her name is Piano with the I removed). Zeno Clash 2 used the same symbols. A sequence of ruined piano, grandfather clock, and something else I don't recall.

1:56 caged bird in the background.

2:20 Tree thing is messing with the model rocket. Father kills it. This is like Vincent Law trying to remember the Boomerang Star spaceship in the MCQ episode, and Proxy One blinding the keeper of the memory.

3:00 She puts on the orange coat herself, and is transported to another world.