[step:Estimate the commutator pairing by the regularity of $Pu$]
For fixed $\tau>0$, the regularization makes the following identity legitimate. Put
\begin{align*}
Q_\tau=A_\tau^*A_\tau.
\end{align*}
Since the $L^2(X)$ inner product is linear in the first argument,
\begin{align*}
\bigl(i(P^*Q_\tau-Q_\tau P)u,u\bigr)_{L^2(X)}=2\operatorname{Im}\bigl(A_\tau Pu,A_\tau u\bigr)_{L^2(X)}.
\end{align*}
The order-$2s$ terms coming from the skew-adjoint part of $P$ and the commutators created by the regularizing family are not added again at this stage; by the formalized commutator package they are already included in the decomposition into $B_\tau^*B_\tau-E_\tau^*E_\tau+R_\tau+F_\tau$, with the absorbable part placed into the small multiple of $B_\tau^*B_\tau$ and the remaining lower-order part placed into $R_\tau+F_\tau$.
Let
\begin{align*}
G\in\Psi^{s-m+1}(X)
\end{align*}
be a properly supported microlocal cutoff that is elliptic on the operator wavefront set of $A$. Let
\begin{align*}
G^{-1}\in\Psi^{-s+m-1}(X)
\end{align*}
denote a microlocal parametrix for $G$ on that conic set. Thus there are properly supported smoothing operators $S_1,S_2\in\Psi^{-\infty}(X)$ microlocally near $\operatorname{WF}'(A)$ such that $G^{-1}G=I+S_1$ and $GG^{-1}=I+S_2$ there. Since $Pu$ is microlocally in $H^{s-m+1}$ on $V$ and the operator wavefront set of $A$ is contained in $V$, we have $GPu\in L^2(X)$. Microlocally on $\operatorname{WF}'(A)$ we may write
\begin{align*}
A_\tau Pu=A_\tau G^{-1}GPu+A_\tau S_1Pu+S_{\tau}u,
\end{align*}
where $S_{\tau}\in\Psi^{-\infty}(X)$ is uniformly smoothing after insertion of a cutoff supported in $\Omega$. The term $A_\tau S_1Pu+S_\tau u$ is therefore bounded by a fixed local negative Sobolev norm of $u$, after choosing $M>0$ so large that $u\in H^{-M}_{\mathrm{loc}}(X)$. The composition $A_\tau G^{-1}$ has order
\begin{align*}
s-(m-1)/2-s+m-1=(m-1)/2.
\end{align*}
Thus $A_\tau Pu$ is paired in $H^{-(m-1)/2}$ against $A_\tau u$ in $H^{(m-1)/2}$, rather than by an $L^2$-boundedness assertion for $A_\tau G^{-1}$. Since the formalized commutator package requires $B$ to be elliptic on a conic neighbourhood of $\operatorname{WF}'(A)$, we choose the support of $G$ inside that elliptic neighbourhood. The uniform microlocal domination estimate included in the package gives
\begin{align*}
\|A_\tau u\|_{H^{(m-1)/2}_{\mathrm{loc}}(X)}\leq C\|B_\tau u\|_{L^2(X)}+C\|u\|_{H^{-M}_{\mathrm{loc}}(X)},
\end{align*}
with $C$ independent of $\tau$. Also $GPu\in L^2(X)$, and the operator $A_\tau G^{-1}$ has order $(m-1)/2$, so $A_\tau Pu$ is bounded in $H^{-(m-1)/2}_{\mathrm{loc}}(X)$ by $\|GPu\|_{L^2(X)}$ plus a fixed local negative Sobolev norm of $u$. Sobolev duality between $H^{-(m-1)/2}_{\mathrm{loc}}(X)$ and $H^{(m-1)/2}_{\mathrm{loc}}(X)$, followed by the Cauchy-Schwarz inequality and the Young inequality $2xy\leq \eta x^2+\eta^{-1}y^2$, gives, for every fixed $\eta>0$,
\begin{align*}
2|\operatorname{Im}(A_\tau Pu,A_\tau u)_{L^2(X)}|\leq \eta\|B_\tau u\|_{L^2(X)}^2+C_{\eta,0}\|GPu\|_{L^2(X)}^2+C_{\eta,1}\|u\|_{H^{-M}_{\mathrm{loc}}(X)}^2.
\end{align*}
Here $M>0$ is fixed large enough that the distribution $u$ belongs locally to $H^{-M}$, the constants $C_{\eta,0},C_{\eta,1}>0$ depend on $\eta$, the chosen microlocal cutoffs, the parametrix $G^{-1}$, and finitely many uniform seminorms of $A_\tau G^{-1}$, but are independent of $\tau$.
This estimate is the point where the hypothesis on $Pu$ is used. The Sobolev order $s-m+1$ is exactly the order that pairs with the order $s$ positive square produced by the commutator of an order-$m$ operator.
[/step]