[step:Handle bounded universal quantifiers and complete the induction]
Assume the induction invariant holds for $\theta(x,y,z_1,\dots,z_k)$, and let $\psi(y,z_1,\dots,z_k)$ be the bounded universal formula
\begin{align*}
\forall x\in y\,\theta(x,y,z_1,\dots,z_k).
\end{align*}
Let $s$ be an assignment with $s(y)\in M$ and $s(z_i)\in M$ for each $i\in\{1,\dots,k\}$. Define $b:=s(y)$. As before, transitivity of $M$ gives
\begin{align*}
\{c\in M:c\in b\}=b.
\end{align*}
Therefore
\begin{align*}
(M,\in)\models \forall x\in y\,\theta[s]
&\iff \text{for every }c\in M\text{ with }c\in b,\ (M,\in)\models \theta[s[x\mapsto c]] \\
&\iff \text{for every }c\in b,\ (M,\in)\models \theta[s[x\mapsto c]] \\
&\iff \text{for every }c\in b,\ V\models \theta[s[x\mapsto c]] \\
&\iff V\models \forall x\in y\,\theta[s].
\end{align*}
Again the induction hypothesis applies because each $c\in b$ lies in $M$.
Thus the induction invariant holds for atomic formulas, is preserved by Boolean connectives, and is preserved by bounded existential and bounded universal quantification. Since every $\Delta_0$ formula is built from atomic formulas using only these operations, the invariant holds for every $\Delta_0$ formula. Applying it to $\varphi(x_1,\dots,x_n)$ with $s(x_i)=a_i$ gives
\begin{align*}
(M,\in)\models\varphi(a_1,\dots,a_n)
\iff
V\models\varphi(a_1,\dots,a_n),
\end{align*}
which is the desired absoluteness.
[/step]