[guided]The purpose of introducing $C_r(t)$ is to separate the fixed prefix $a_0,\dots,a_r$ from the final input $t$. Once this dependence is written as a linear fractional function of $t$, the usual recurrence appears by substituting the next partial quotient.
When $n \geq 1$, fix $r$ with $0 \leq r \leq n-1$. Define $C_r$ to be the map from $\mathbb{Q}_{>0}$ to $\mathbb{Q}$ given by
\begin{align*}
C_r(t) := [a_0;a_1,\dots,a_r,t].
\end{align*}
We prove
\begin{align*}
C_r(t)=\frac{t p_r+p_{r-1}}{t q_r+q_{r-1}}
\end{align*}
by induction on $r$.
For $r=0$, the continued fraction has only the prefix entry $a_0$ and the variable final entry $t$. Therefore
\begin{align*}
C_0(t)
= [a_0;t]
= a_0+\frac{1}{t}
= \frac{t a_0+1}{t}.
\end{align*}
The recurrence already gave $p_0=a_0$, $p_{-1}=1$, $q_0=1$, and $q_{-1}=0$, so this is exactly
\begin{align*}
C_0(t)=\frac{t p_0+p_{-1}}{t q_0+q_{-1}}.
\end{align*}
Now assume the formula is known for $r-1$, where $1 \leq r \leq n-1$. The final two entries of
\begin{align*}
[a_0;a_1,\dots,a_r,t]
\end{align*}
combine into one positive rational number. Define
\begin{align*}
s := a_r+\frac{1}{t}.
\end{align*}
Because $a_r \in \mathbb{N}$ and $t>0$, the number $s$ is positive, so it is a valid input for the induction hypothesis. By the recursive definition of finite continued fractions,
\begin{align*}
C_r(t)=[a_0;a_1,\dots,a_{r-1},s].
\end{align*}
The induction hypothesis gives
\begin{align*}
C_r(t)
= \frac{s p_{r-1}+p_{r-2}}{s q_{r-1}+q_{r-2}}.
\end{align*}
This quotient is defined because $s>0$ and $q_{r-1}>0$ by the first step. We also have $q_{r-2}\geq 0$: if $r=1$, then $q_{r-2}=q_{-1}=0$, while if $r\geq 2$, then $q_{r-2}>0$ by the positivity already proved. Hence
\begin{align*}
s q_{r-1}+q_{r-2}>0.
\end{align*}
Substituting
\begin{align*}
s=a_r+\frac{1}{t}
\end{align*}
gives
\begin{align*}
C_r(t)
= \frac{\left(a_r+\frac{1}{t}\right)p_{r-1}+p_{r-2}}
{\left(a_r+\frac{1}{t}\right)q_{r-1}+q_{r-2}}.
\end{align*}
Since $t>0$, multiplying both numerator and denominator by $t$ does not change the quotient. Hence
\begin{align*}
C_r(t)= \frac{t(a_rp_{r-1}+p_{r-2})+p_{r-1}}
{t(a_rq_{r-1}+q_{r-2})+q_{r-1}}.
\end{align*}
The expressions in parentheses are exactly the recurrence definitions
\begin{align*}
p_r=a_rp_{r-1}+p_{r-2},\qquad q_r=a_rq_{r-1}+q_{r-2}.
\end{align*}
Therefore
\begin{align*}
C_r(t)=\frac{t p_r+p_{r-1}}{t q_r+q_{r-1}},
\end{align*}
which completes the induction.[/guided]