This is an exercise from Kanamori's "The Higher Infinite" which I solved by strengthening the hypothesis and I would like to know how we can solve it without doing that.
So the exercise is:
Exercise. Suppose that $\kappa \lt \lambda$, $\lambda$ is a strong limit of cofinality $\omega$, and there is a $j:V\prec M$ with $\operatorname{crit}(j) = \kappa$ and $V_\lambda \subseteq M$. Let $\mathcal{E}$ be the $(\kappa, \lambda)$-extender derived from $j$ and $j_\mathcal{E}:V\prec M_\mathcal{E}$. Then $^\omega M_\mathcal{E} \not \subseteq M_\mathcal{E}$.
Hint. $V_\lambda \subseteq M_\mathcal{E}$ by $(*)$, and so if $\kappa \le \beta \lt \lambda$, the $(\kappa, \beta)$-extender $\mathcal{E}|[\beta]^{\lt \omega} \in M_\mathcal{E}$. But $\mathcal{E} \not \in M_\mathcal{E}$.
The $(*)$ that is being referred to is:
$(*)$. Suppose we are working with a $N$-$(\kappa, \beta)$-extender $\mathcal{E}$ derived from some $j:N\prec M$. Then for any $\gamma$ satisfying $|V_\gamma|^M \le \beta$, we have $V_\gamma^M = V_\gamma^{M_\mathcal{E}}$.
This exercise seems quite straight-forward, especially with hint. But when I tried to show that $|V_\lambda|^M \le \lambda$, I ran into cofinality issues.
What I did was, I assumed that $\lambda$ was the limit of an $\omega$-sequence of inaccessibles and that did the job. Because inaccessibility is downward-absolute for inner models of ZFC, for each $\alpha \lt \lambda$ we can bound $|V_\alpha|^M$ with the size of the inaccessible cardinal above it, which in turn is less than $\lambda$. And we are done.
My question is: Can we say this for general strong limits?
It is true that it may happen that $\vert V_\lambda\vert^M>\lambda$. Note that the additional assumption you made is overkill for your argument: One can show that for $\alpha>\omega$, $\vert V_\alpha\vert=\alpha$ if and only if $\beth_\alpha=\alpha$. So you could also assume that $\lambda$ is a $\beth$-fixed point and then it is quite easy to see that $\lambda$ is a $\beth$-fixed point in $M$ as well (observe that the $\beth$-fixed points form a club and that $(\beth\upharpoonright\lambda)^V=(\beth\upharpoonright\lambda)^M$). Furthermore, a limit of inaccessibles is always a $\beth$-fixed point as all inaccessibles are $\beth$-fixed points, so this assumption is really less restrictive.
Anyhow the exercise is true without any additional assumption. To see that, we will code the extender more "rank-efficient". Let $\gamma$ be the maximal ordinal $\alpha$ with $\vert V_\alpha\vert^M\leq\lambda$. I claim that $\gamma$ is a limit of countable cofinality in $V$ and satisfies $\vert V_\gamma\vert^M=\lambda$. First note that the function $h(\alpha)=\vert V_\alpha\vert^M$ is strictly increasing and continuous (so normal) map (it is just the function $(\omega+\alpha\mapsto\beth_{\alpha})^M)$. So if $\alpha<\gamma$ then $\vert V_\alpha\vert^M<\lambda$. As $\lambda$ is a strong limit in $V$ and $V_\lambda\subseteq M$, $\lambda$ is a strong limit in $M$ as well. Thus $\vert V_{\alpha+1}\vert^M=(2^{\vert V_\alpha\vert})^M<\lambda$. Hence $\gamma$ is a limit. The rest of the claim follows from the normality of $h$.
Thus we may take a bijecion $f:V_\gamma\rightarrow\lambda$ in $M$; we will even take $f$ in $M_{\mathcal E}$ (note that $V_\gamma$ is the same in $V$, $M$ and $M_{\mathcal E}$ and has size $\lambda$ everywhere as well). We will moreover assume that whenever $\alpha<\gamma$ then $f\upharpoonright V_\alpha$ is a bijection between $V_\alpha$ and $\vert V_\alpha\vert$. We will now code the $(\kappa, \lambda)$ extender $E$, which is a directed system of ultrafilters indexed by $a\in[\lambda]^{<\omega}$ as a "$(\kappa, V_\gamma)$"-extender $F$ indexed by $a\in [V_\gamma]^{<\omega}$. Just put, for $a\in [V_\gamma]^{<\omega}$, $$F_a=\{\{(f^{-1}(b_0), \dots, f^{-1}(b_{\vert a\vert-1}))\mid (b_0,\dots, b_{\vert a\vert-1})\in A\}\mid A\in E_{f"a}\}$$ Here, I understand $E_{f"a}$ to be an ultrafilter on $[\xi]^{\vert a\vert}$ for $\xi$ least with $j(\xi)>\operatorname{max}f"a$ (so that $\xi<\lambda$). By our assumption on $f$, $F_a\subseteq V_\alpha$ for some $\alpha<\gamma$ only depending on and increasing in $\operatorname{max} f"a$, so that $F\upharpoonright[V_\beta]^{<\omega}\in V_\gamma$ whenever $\beta<\gamma$. Finally, let $(\gamma_n)_{n<\omega}$ be a sequence in $V$, witnessing $\gamma$ to have countable cofinality. We have $F\upharpoonright [V_{\gamma_n}]^{<\omega}\in V_\gamma\subseteq M_\mathcal E$ for all $n<\omega$, however $F\notin M_\mathcal E$ as otherwise $M_\mathcal E$ could decode $E$ from $F$ using $f$.
Edit: Regarding the questions: