[guided]The point of taking the $L^2$ inner product with $\alpha$ is that the second-order operator $\Delta_{\bar\partial}$ becomes a sum of first-order energies. The operator $\bar\partial^*$ is defined as the formal adjoint of $\bar\partial$ for the fixed Hermitian metric $g$, so for smooth forms $\beta$ and $\gamma$ of compatible bidegrees we have
\begin{align*}
(\bar\partial\beta,\gamma)_{L^2}=(\beta,\bar\partial^*\gamma)_{L^2}.
\end{align*}
We apply this identity to the first term in the expansion of the Laplacian. Since $\alpha\in A^{p,q}(X)$, the form $\bar\partial^*\alpha$ lies in $A^{p,q-1}(X)$, and $\bar\partial(\bar\partial^*\alpha)$ lies in $A^{p,q}(X)$, so the inner product with $\alpha$ is defined. With $\beta=\bar\partial^*\alpha$ and $\gamma=\alpha$, the adjoint identity gives
\begin{align*}
(\bar\partial\bar\partial^*\alpha,\alpha)_{L^2}=(\bar\partial^*\alpha,\bar\partial^*\alpha)_{L^2}.
\end{align*}
By the definition of the $L^2$ norm, this is
\begin{align*}
(\bar\partial\bar\partial^*\alpha,\alpha)_{L^2}=\|\bar\partial^*\alpha\|_{L^2}^2.
\end{align*}
For the second term, use the same adjoint relation with the roles shifted. Since $\bar\partial\alpha\in A^{p,q+1}(X)$, applying $\bar\partial^*$ to $\bar\partial\alpha$ gives a form in $A^{p,q}(X)$. Taking $\eta=\bar\partial\alpha$ and $\theta=\alpha$, the adjoint identity gives
\begin{align*}
(\bar\partial^*\bar\partial\alpha,\alpha)_{L^2}=(\bar\partial\alpha,\bar\partial\alpha)_{L^2}.
\end{align*}
Again by the definition of the $L^2$ norm,
\begin{align*}
(\bar\partial^*\bar\partial\alpha,\alpha)_{L^2}=\|\bar\partial\alpha\|_{L^2}^2.
\end{align*}
Combining the two displayed identities with
\begin{align*}
\Delta_{\bar\partial}\alpha=\bar\partial\bar\partial^*\alpha+\bar\partial^*\bar\partial\alpha
\end{align*}
yields the energy identity
\begin{align*}
(\Delta_{\bar\partial}\alpha,\alpha)_{L^2}=\|\bar\partial\alpha\|_{L^2}^2+\|\bar\partial^*\alpha\|_{L^2}^2.
\end{align*}
This identity is the whole mechanism of the criterion: the left side records harmonicity, while the right side is a sum of nonnegative squared norms.[/guided]