I am currently studying the textbook Partial Differential Equations – An introduction, second edition, by Walter A. Strauss. The section The Variable Coefficient Equation of chapter 1 says the following:
The equation $$u_x + y u_y = 0 \label{4}\tag{4}$$ is linear and homogeneous but has a variable coefficient ($y$). We shall illustrate for equation \eqref{4} how to use the geometric method somewhat like Example 1. The PDE \eqref{4} itself asserts that the directional derivative in the direction of the vector $(1, y)$ is zero. The curves in the $xy$ plane with $(1, y)$ as tangent vectors have slopes $y$ (see Figure 3). Their equations are $$\dfrac{dy}{dx} = \dfrac{y}{1} \label{5}\tag{5}$$ This ODE has the solutions $$y = Ce^x \label{6}\tag{6}$$ These curves are called the characteristic curves of the PDE \eqref{4} . As $C$ is changed, the curves fill out the $xy$ plane perfectly without intersecting. On each of the curves $u(x, y)$ is a constant because $$\dfrac{d}{dx}u(x, Ce^x) = \dfrac{\partial{u}}{\partial{x}} + Ce^x \dfrac{\partial{u}}{\partial{y}} = u_x + yu_y = 0.$$ Thus $u(x, Ce^x) = u(0, Ce^0) = u(0, C)$ is independent of $x$. Putting $y = Ce^x$ and $C = e^{−x}y$, we have $$u(x, y) = u(0, e^{-x}y).$$ It follows that $$u(x, y) = f(e^{-x}y) \label{7}\tag{7}$$ is the general solution of this PDE, where again $f$ is an arbitrary function of only a single variable. This is easily checked by differentiation using the chain rule (see Exercise 4). Geometrically, the “picture” of the solution $u(x, y)$ is that it is constant on each characteristic curve in Figure 3.
I am now trying to do the following exercise:
Find the solution of \eqref{4} that satisfies the auxiliary equation $u(0, y) = y^3$.
I used \eqref{6} to get that $u(0, y) = y = C$, which means that $y = C = y^3$. However, I think that this is an incorrect conclusion. But is this not the reasoning that the author applied above to get \eqref{7}? So I don't understand why this reasoning was incorrect in this case.
I would greatly appreciate it if people would please take the time to carefully explain this.

You seem to make some confusion due to the use of the variables $x,y$ for multiple (and different) purposes. The auxiliary (initial value) equation you write as $u(0,y)=y^3$ but you could equally well write it as $u(0,t)=t^3$ for any real value of $t$ (better not use $y$ here).
For a given point $(x,y)$ in the plane you have from the result just before (7): $u(x,y) = u(0,ye^{-x})$. Setting $t=y e^{-x}$ and using the previous we get:
$$ u(x,y)=u(0,ye^{-x}) = u(0,t) = t^3 = (y e^{-x})^3 = y^3 e^{-3x}.$$
Hope this brings you some peace of mind.