One approach to handle this question is to note that every matrix has a unique reduced row echelon form (rref): For every matrix $A\in M_{m,n}(\mathbb{R})$, if $\hat{A}\in M_{m,n}(\mathbb{R})$ is the rref of $A$, there exists an elementary matrix $S\in M_m(\mathbb{R})$ such that $\hat{A}=SA$.
Here $S$ reflect the elementary row operations needed to recover $A$ from $\hat{A}$. To obtain such $S$, one may consider the augmented matrix $(A\mid I_3)$. Observe that $$S(A\mid I_3)=(SA\mid SI_3)=(\hat{A}\mid S).$$ Then it suffices to compute the rref of $A$ along with the augmented matrix $(A\mid I_3)$.
First, we may find the rref of $M_B^A$:
\begin{align*}
(M_B^A\mid I_3)&=\begin{pmatrix} 1 & 2 & 3 & 1 & 0 & 0 \\ 4 & 5 & 6 & 0 & 1 & 0 \\ 7 & 8 & 9 & 0 & 0 & 1 \end{pmatrix}\xrightarrow{r_3\gets r_3-r_2}\begin{pmatrix} 1 & 2 & 3 & 1 & 0 & 0 \\ 4 & 5 & 6 & 0 & 1 & 0 \\ 3 & 3 & 3 & 0 & -1 & 1 \end{pmatrix} \\
&\xrightarrow{r_2\gets r_2-r_1}\begin{pmatrix} 1 & 2 & 3 & 1 & 0 & 0 \\ 3 & 3 & 3 & -1 & 1 & 0 \\ 3 & 3 & 3 & 0 & -1 & 1 \end{pmatrix}\xrightarrow{r_3\gets r_3-r_2}\begin{pmatrix} 1 & 2 & 3 & 1 & 0 & 0 \\ 3 & 3 & 3 & -1 & 1 & 0 \\ 0 & 0 & 0 & 1 & -2 & 1 \end{pmatrix} \\
&\xrightarrow{r_2\gets r_2-3r_1}\begin{pmatrix} 1 & 2 & 3 & 1 & 0 & 0 \\ 0 & -3 & -6 & -4 & 1 & 0 \\ 0 & 0 & 0 & 1 & -2 & 1 \end{pmatrix}\xrightarrow{r_2\gets r_2/(-3)}\begin{pmatrix} 1 & 2 & 3 & 1 & 0 & 0 \\ 0 & 1 & 2 & 4/3 & -1/3 & 0 \\ 0 & 0 & 0 & 1 & -2 & 1 \end{pmatrix} \\
&\xrightarrow{r_1\gets r_1-2r_2}\begin{pmatrix} 1 & 0 & -1 & -5/3 & 2/3 & 0 \\ 0 & 1 & 2 & 4/3 & -1/3 & 0 \\ 0 & 0 & 0 & 1 & -2 & 1 \end{pmatrix}.
\end{align*}
This shows that
$$X_1:=\begin{pmatrix} 1 & 0 & -1 \\ 0 & 1 & 2 \\ 0 & 0 & 0 \end{pmatrix}=\boxed{\begin{pmatrix} -5/3 & 2/3 & 0 \\ 4/3 & -1/3 & 0 \\ 1 & -2 & 1 \end{pmatrix}}M_B^A=:\boxed{S_1}M_B^A.$$
By similar arguments, we also have
$$X_2:=\begin{pmatrix} 1 & 0 & -2 \\ 0 & 1 & -1 \\ 0 & 0 & 0 \end{pmatrix}=\boxed{\begin{pmatrix} 1/4 & 1/2 & 0 \\ -1/8 & 1/4 & 0 \\ -1/4 & -1/2 & 1 \end{pmatrix}}M_E^E=:\boxed{S_2}M_E^E.$$
Now we may make some further observations: Here $X_1=S_1M_B^A$ where $S_1,S_2$ are non-singular, so we have $M_B^A=S_1^{-1}X_1$. Because $X_1$ and $X_2$ are in rref, if we can find another non-singular matrix $T$ such that $X_1=X_2T$, then $$M_B^A=S_1^{-1}X_1=S_1^{-1}X_2T=S_1^{-1}S_2M_E^ET.$$
To find such $T$, one can consider the dual version of our previous argument by performing elementary column operations to $\begin{pmatrix} X_1 \\ I_3 \end{pmatrix}$ and $\begin{pmatrix} X_2 \\ I_3 \end{pmatrix}$, and multiply the corresponding elementary matrices in some fashion.
In this question, however, some easy observations are sufficient as the structures of $X_1$ and $X_2$ are rather simple:
$$X_1=\begin{pmatrix} 1 & 0 & -1 \\ 0 & 1 & 2 \\ 0 & 0 & 0 \end{pmatrix}=\begin{pmatrix} 1 & 0 & -2 \\ 0 & 1 & -1 \\ 0 & 0 & 0 \end{pmatrix}\boxed{\begin{pmatrix} 1 & 0 & 1 \\ 0 & 1 & 3 \\ 0 & 0 & 1 \end{pmatrix}}=X_2\boxed{T}$$
Let me explain how I found such $T$:
Because the first two columns of $X_1$ and $X_2$ are identical, we can then put the first two columns of $T$ to be simply $(1,0,0)^T$ and $(0,1,0)^T$.
Now since $T$ is supposed to be non-singular, I can put the last column to be of the form $(x,y,1)^T$ (here $1$ of course can be replaced by other real numbers). Then by solving linear systems, I got $x=1$ and $y=3$.
As a result, such $T$ is not necessarily unique, so it is possible for you to find different solutions.
Anyway, now we may let
$$T_B^E:=S_1^{-1}S_2=\begin{pmatrix} -5/3 & 2/3 & 0 \\ 4/3 & -1/3 & 0 \\ 1 & -2 & 1 \end{pmatrix}^{-1}\begin{pmatrix} 1/4 & 1/2 & 0 \\ -1/8 & 1/4 & 0 \\ -1/4 & -1/2 & 1 \end{pmatrix}=\boxed{\begin{pmatrix} 0 & 1 & 0 \\ 3/8 & 13/4 & 0 \\ 1/2 & 5 & 1 \end{pmatrix}}$$
and
$$T_E^A:=T=\boxed{\begin{pmatrix} 1 & 0 & 1 \\ 0 & 1 & 3 \\ 0 & 0 & 1 \end{pmatrix}}.$$
As noted above, we now have
$$M_B^A=S_1^{-1}S_2M_E^ET=T_B^EM_E^ET_E^A.$$
P.S. Here are some theories: Let $A\in M_{m,n}(\mathbb{R})$ be of rank $r$. Then there exist non-singular matrices $P\in M_m(\mathbb{R})$ and $Q\in M_n(\mathbb{R})$ such that
$$A=P\begin{pmatrix} I_r & 0_{r\times(n-r)} \\ 0_{(m-r)\times(n-r)} & 0_{(m-r)\times(n-r)} \end{pmatrix}Q.$$
Here $P$ can be obtained by performing elementary row operations to $A$ to find rref, and $Q$ can be obtained by continuing with elementary column operations.
If $B\in M_{m,n}(\mathbb{R})$ represents the same linear transformation as $A$ with respect to different bases, then the rank of $B$ is also equal to $r$, and certainly, we can find $P\in M_m(\mathbb{R})$ and $Q\in M_n(\mathbb{R})$ such that
\begin{align*}
B&=P'\begin{pmatrix} I_r & 0_{r\times(n-r)} \\ 0_{(m-r)\times(n-r)} & 0_{(m-r)\times(n-r)} \end{pmatrix}Q' \\
&=P'(P^{-1}AQ^{-1})Q'=\boxed{(P'P^{-1})}A\boxed{(Q^{-1}Q')}.
\end{align*}