By the way, you are right to have some qualms, since in general, $[X,Y,Z]=[[X,Y],Z]$ is not generated by elements of the form $[[x,y],z]$ with $x\in X$, $y\in Y$, $z\in Z$, even though $[X,Y]$ is generated by elements $[x,y]$ with $x\in X$ and $y\in Y$. So there is something a bit special about the sets involved here.
I think the key is something like this:
Theorem. If $G=\langle Y\rangle$ and $N=\langle X\rangle^G$ for subsets $X$ and $Y$ of $G$, then $[N,G]=[X,Y]^G$.
(This is Proposition 1.2.8 in Susan McKay’s Finite $p$-groups, Queen Mary Maths Notes 18)
Here, $H^G$ for subgroup $H$ means the normal closure of $H$ in $G$, and $[X,Y] = \langle [x,y]\mid x\in X, y\in Y\rangle$.
Now, taking $N=G=X=Y$ gives that $[G,G]$ is the normal closure of the subgroup generated by the commutators; but since $[x,y]^g = [x^g,y^g]$, this subgroup is already normal.
Now, we can replace $G$ with $G’$, $N$ with $G’$, and let $X=Y=\{[x,y]\mid x,y\in G\}$. We note that $X$ and $Y$ are closed under conjugation. Then $[G’,G’] = [X,Y]^G = [X,Y]$ is generated by elements of the form $\bigl[ [x,y],[z,w]\bigr]$.
Then we apply the theorem taking $G$ and $N$ to be $G’’$, and taking $X$ and $Y$ to be the set of commutators-of-commutators, $[[x,y],[z,w]]$. Etc.
To prove the theorem: let’s state the commutator identities:
$$\begin{align*}
[y,x]^{-1} &= [x,y] \\
[xy,z] &= [x,z]^y[y,z]\\
[x,yz] &= [x,z][x,y]^z\\
[x,y^{-1}] &= [y,x]^{y^{-1}}\\
[x^{-1},y] &= [y,x]^{x^{-1}}
\end{align*}$$
My commutator convention is that $[x,y]=x^{-1}y^{-1}xy$; if your convention is $[x,y]=xyx^{-1}y^{-1}$ you need to tweak the identities above.
Now, clearly each element of the generating set of $[X,Y]$ lies in $[N,G]$, which is normal, so $[X,Y]^G$ is contained in $[N,G]$. Thanks to the commutator identities, every element of $[N,G]$ is a product of conjugates of powers of elements of
the form $[x^z,y]$ with $x\in X$, $y\in Y$, and $z\in G$. Since $[x^z,y] = [x,y^{z^{-1}}]^z$ and $y^{z^{-1}}\in\langle Y\rangle$, the commutator identities show that $[N,G]\subseteq [X,Y]^G$, giving the desired equality.