Based on examples from the online textbook, I am pretty sure we are allowed to integrate at that stage. Also Example 2 b from Section 2.6 seems to discard the constants of integration so I will follow that convention. Here is my solution to part 1:
We know $u(x,t)$ is of the form $u(x,t) = \varphi(x+ct)+\psi(x-ct)$.
For $x>ct$ we use the initial conditions:
\begin{align}
u|_{t=0}= \phi (x)
&\implies \varphi(x)+\psi(x) = \phi(x) \\
u_t|_{t=0}= c\phi'(x)
&\implies \varphi'(x)-\psi'(x)=\phi'(x)
\end{align}
Therefore $\varphi(x)=\phi(x)$ and $\psi(x)=0$ when $x>0$. So
\begin{equation}
u(x,t) = \phi(x+ct), \quad
\text{when } x>ct
\end{equation}
For $0<x<ct$ we use the boundary condition:
\begin{align}
(u_x+\alpha u_t)|_{x=0}=0
&\implies \varphi'(ct) + \psi'(-ct)
+ \alpha c\varphi'(ct) -\alpha c\psi'(-ct) = 0 \\
&\implies \frac{1}{c}\varphi(ct) - \frac{1}{c}\psi(-ct)
+ \alpha \varphi(ct) +\alpha\psi(-ct) = k
\end{align}
Letting $t=-\frac{x}{c}$ and rearranging yields
\begin{align}
\psi(x) &= - \left(
\frac{\alpha c + 1}{\alpha c -1} \right)
\varphi(-x) + k, \quad
\text{for } x<0 \\
&= - \left(
\frac{\alpha c + 1}{\alpha c -1} \right)
\phi(-x) + k
\end{align}
So
\begin{equation}
u(x,t) = \phi(x+ct)- \left(
\frac{\alpha c + 1}{\alpha c -1} \right)
\phi(ct-x), \quad
\text{when } 0<x<ct
\end{equation}
(we set $k=0$ so that $u$ is continuous at $x=ct$)
Therefore,
\begin{equation}
u(x,t) =
\left\{ \begin{aligned}
&\phi(x+ct), &&x>ct \\
&\phi(x+ct) - \left(
\frac{\alpha c + 1}{\alpha c -1} \right)
\phi(ct-x), &&0<x<ct
\end{aligned}
\right.
\end{equation}