[proofplan]
We compare the two representing isomorphisms by forming the natural isomorphism $\tau:=\beta^{-1}\circ\alpha$ from $\operatorname{Hom}_{\mathcal C}(-,A)$ to $\operatorname{Hom}_{\mathcal C}(-,B)$. Naturality forces $\tau$ to be postcomposition by the single morphism $f:=\tau_A(\operatorname{id}_A):A\to B$. Applying the same construction to $\tau^{-1}$ produces a morphism $g:B\to A$, and the two natural transformations being inverse implies $g\circ f=\operatorname{id}_A$ and $f\circ g=\operatorname{id}_B$. Finally, the compatibility equation determines $f$ by evaluating at $X=A$ and $u=\operatorname{id}_A$.
[/proofplan]
[step:Compare the two representing isomorphisms by a natural isomorphism of Hom functors]
Define a natural transformation
\begin{align*}
\tau:\operatorname{Hom}_{\mathcal C}(-,A)&\longrightarrow \operatorname{Hom}_{\mathcal C}(-,B)
\end{align*}
by
\begin{align*}
\tau_X:=\beta_X^{-1}\circ \alpha_X
\end{align*}
for each object $X\in \operatorname{Ob}(\mathcal C)$. Since $\alpha$ and $\beta$ are natural isomorphisms, each component $\tau_X$ is a bijection, and $\tau$ is a natural isomorphism. Thus, for every morphism $r:Y\to X$ in $\mathcal C$, the naturality square says that for every $u:X\to A$,
\begin{align*}
\tau_Y(u\circ r)=\tau_X(u)\circ r.
\end{align*}
[/step]
[step:Recover the morphism $A\to B$ from the image of the identity]
Define the morphism
\begin{align*}
f:A&\longrightarrow B
\end{align*}
by
\begin{align*}
f:=\tau_A(\operatorname{id}_A).
\end{align*}
We claim that $\tau$ is postcomposition by $f$. Let $X\in \operatorname{Ob}(\mathcal C)$ and let $u:X\to A$ be a morphism. Apply the naturality identity for $\tau$ to the morphism $u:X\to A$ and to $\operatorname{id}_A\in \operatorname{Hom}_{\mathcal C}(A,A)$. This gives
\begin{align*}
\tau_X(u)
&=\tau_X(\operatorname{id}_A\circ u)\\
&=\tau_A(\operatorname{id}_A)\circ u\\
&=f\circ u.
\end{align*}
Therefore, for every object $X$ and every morphism $u:X\to A$,
\begin{align*}
\beta_X^{-1}(\alpha_X(u))=\tau_X(u)=f\circ u.
\end{align*}
Applying $\beta_X$ to both sides yields the desired compatibility relation
\begin{align*}
\beta_X(f\circ u)=\alpha_X(u).
\end{align*}
[guided]
The natural isomorphism $\tau$ contains all the information comparing the two representing objects. To extract an actual morphism $A\to B$, we evaluate $\tau$ at the object $A$ and at the distinguished element $\operatorname{id}_A\in \operatorname{Hom}_{\mathcal C}(A,A)$. Define
\begin{align*}
f:A&\longrightarrow B
\end{align*}
by
\begin{align*}
f:=\tau_A(\operatorname{id}_A).
\end{align*}
Now we show that this single morphism controls every component of $\tau$. Let $X\in \operatorname{Ob}(\mathcal C)$ and let $u:X\to A$ be a morphism. Since $\operatorname{Hom}_{\mathcal C}(-,A)$ and $\operatorname{Hom}_{\mathcal C}(-,B)$ are contravariant Hom functors, the morphism $u:X\to A$ induces maps by precomposition:
\begin{align*}
\operatorname{Hom}_{\mathcal C}(A,A)&\longrightarrow \operatorname{Hom}_{\mathcal C}(X,A),\\
h&\longmapsto h\circ u,
\end{align*}
and
\begin{align*}
\operatorname{Hom}_{\mathcal C}(A,B)&\longrightarrow \operatorname{Hom}_{\mathcal C}(X,B),\\
k&\longmapsto k\circ u.
\end{align*}
Naturality of $\tau$ with respect to $u:X\to A$ therefore gives
\begin{align*}
\tau_X(\operatorname{id}_A\circ u)=\tau_A(\operatorname{id}_A)\circ u.
\end{align*}
Since $\operatorname{id}_A\circ u=u$ and $\tau_A(\operatorname{id}_A)=f$, this becomes
\begin{align*}
\tau_X(u)=f\circ u.
\end{align*}
Because $\tau_X=\beta_X^{-1}\circ\alpha_X$, we have
\begin{align*}
\beta_X^{-1}(\alpha_X(u))=f\circ u.
\end{align*}
Applying the bijection $\beta_X$ to both sides gives
\begin{align*}
\beta_X(f\circ u)=\alpha_X(u).
\end{align*}
This is exactly the compatibility condition in the statement.
[/guided]
[/step]
[step:Construct the inverse morphism from the inverse natural isomorphism]
Let
\begin{align*}
\sigma:\operatorname{Hom}_{\mathcal C}(-,B)&\longrightarrow \operatorname{Hom}_{\mathcal C}(-,A)
\end{align*}
be the inverse natural isomorphism $\sigma:=\tau^{-1}$. Define
\begin{align*}
g:B&\longrightarrow A
\end{align*}
by
\begin{align*}
g:=\sigma_B(\operatorname{id}_B).
\end{align*}
The same naturality argument applied to $\sigma$ shows that, for every object $X\in \operatorname{Ob}(\mathcal C)$ and every morphism $v:X\to B$,
\begin{align*}
\sigma_X(v)=g\circ v.
\end{align*}
Since $\sigma\circ\tau=\operatorname{id}_{\operatorname{Hom}_{\mathcal C}(-,A)}$, evaluating at $A$ and at $\operatorname{id}_A$ gives
\begin{align*}
\operatorname{id}_A
&=(\sigma_A\circ\tau_A)(\operatorname{id}_A)\\
&=\sigma_A(f)\\
&=g\circ f.
\end{align*}
Since $\tau\circ\sigma=\operatorname{id}_{\operatorname{Hom}_{\mathcal C}(-,B)}$, evaluating at $B$ and at $\operatorname{id}_B$ gives
\begin{align*}
\operatorname{id}_B
&=(\tau_B\circ\sigma_B)(\operatorname{id}_B)\\
&=\tau_B(g)\\
&=f\circ g.
\end{align*}
Thus $g$ is a two-sided inverse for $f$, so $f:A\to B$ is an isomorphism in $\mathcal C$.
[/step]
[step:Prove uniqueness among compatible morphisms]
Let $q:A\to B$ be a morphism satisfying the same compatibility condition: for every object $X\in \operatorname{Ob}(\mathcal C)$ and every morphism $u:X\to A$,
\begin{align*}
\beta_X(q\circ u)=\alpha_X(u).
\end{align*}
Taking $X=A$ and $u=\operatorname{id}_A$, we obtain
\begin{align*}
\beta_A(q)=\alpha_A(\operatorname{id}_A).
\end{align*}
For the morphism $f$ constructed above, the same compatibility condition gives
\begin{align*}
\beta_A(f)=\alpha_A(\operatorname{id}_A).
\end{align*}
Hence
\begin{align*}
\beta_A(q)=\beta_A(f).
\end{align*}
Since $\beta_A:\operatorname{Hom}_{\mathcal C}(A,B)\to F(A)$ is a bijection, it follows that $q=f$. Therefore the compatible isomorphism $A\to B$ is unique.
[/step]