I think the first game between Meek-Morphy tries to illustrate what can happen if you move the same piece twice in the opening and the second game tries to illustrate the downside of pawn moves instead of piece development (especially notice how 4. g4 followed by e5 exposes the weak e1-h4 diagonal).
The exercises in chapter three all have something to do with one side ignoring the principles explained at the start of the chapter (basic opening principles). For instance exercise 3.2 illustrates what can happen if you do not have control of the centre (notice how the pawns can move forward, forcing black to move its pieces to less desirable squares gaining more and more space for white to get the upper hand).
Exercise 3.8 (Bh6) tries to show you how black is unable to bring its king in to safety by blocking the short castling, thus leaving the king stuck in the centre.
If you re-read the chapter and the illustrative games and still have difficulties understanding what is being taught, try to go through the exercises and the answers and move on to the next chapter. After a couple of chapters go back and see if you can now understand why which move is made.
I'm currently working my way through Artur Yupusov's first orange book "Build Up Your Chess: The Fundamentals". I did pretty well in the first two quizzes on checkmate patterns, but I am struggling immensely in the third chapter. In the introduction, Yusupov says that the quizzes should take about 1-2 hours to finish, I spent 4-5 hours on the first 6 puzzles and got 5 of them wrong.
After the quiz, it says that if you got below a certain threshold of points, you should re-read the chapter, but the chapter consists of two games (one by Morphy, one by Yusupov himself), and to tell you the truth, I have no idea how these games have any relation with how to play in the opening. In the quick intro to the chapter, he mentions the rules we all hear "develop your pieces, castle early, control the center, don't move a piece twice etc." yet in both games, pieces are moved multiple times, most pieces don't come out into the fight until the 10th-12th move, etc.
It's a really confusing chapter, and it's getting me frustrated. I'd love if someone could tell me what I should be looking for in a position (I have real difficulties with pawn moves; for example, in one game white has only one piece developed, so I figured that I should be developing more pieces, yet the correct solution was to push one of the central pawns a second time.)