For the even polynomial $P(x) = H_n(x)^2$, you are trying to find a closed form for
$$F(a^2) = \int_{-\infty}^\infty P(ax)e^{-x^2/2}\,dx.$$
Differentiating with respect to $a$,
$$\begin{align*}2aF'(a^2) &= \int_{-\infty}^\infty P'(ax)\,xe^{-x^2/2}\,dx \\
&\mathop{=}^{\text{I.B.P.}}-P'(ax)\,e^{-x^2/2}\left. \right]_{-\infty}^\infty + \int_{-\infty}^\infty aP''(ax)\,e^{-x^2/2}\,dx\\
&= \int_{-\infty}^\infty aP''(ax)\,e^{-x^2/2}\,dx
\end{align*}$$
so
$$F'(a^2) = \frac{1}{2}\int_{-\infty}^\infty P''(ax)\,e^{-x^2/2}\,dx.$$
Repeating this process, we find
$$F^{(k)}(a^2) = \frac{1}{2^k}\int_{-\infty}^\infty P^{(2k)}(ax)\,e^{-x^2/2}\,dx. \tag{1}$$
so
$$\frac{F^{(k)}(0)}{k!} = \frac{\sqrt{2\pi}}{2^k k!}P^{(2k)}(0);$$
in other words the coefficient of $a^{2k}$ in $F(a^2)$ is $\sqrt{2\pi}\frac{(2k)!}{2^k k!}$ times the coefficient of $x^{2k}$ in $P(x)$.
For $P(x) = H_n(x)^2$ we have
$$\frac{P^{(2k)}(x)}{(2k)!} = \sum_{i+j = 2k}\frac{H_n^{(i)}(x)}{i!}\frac{H_n^{(j)}(x)}{j!}.$$
From the identity $H_n^{(m)}(x) = 2^m \frac{n!}{(n-m)!}H_{n-m}(x)$, we get
$$\frac{P^{(2k)}(x)}{(2k)!} = 2^{2k}\sum_{i+j = 2k}\binom{n}{i}\binom{n}{j}H_{n-i}(x)H_{n-j}(x). \tag{2}$$
From here we could plug in $x=0$ to derive an explicit (albeit messy) expression for $F(a^2)$.
Alternatively, we can exploit orthogonality by substituting equation $(2)$ into equation $(1)$ and setting $a = \frac{1}{\sqrt{2}}$. Then all of the terms disappear except for the $i=j=k$ term, and we are just left with
$$ F^{(k)}(1/2) = (2k)!\,2^k\binom{n}{k}^2\int_{-\infty}^\infty \left[H_{n-k}\left(\frac{x}{\sqrt{2}}\right)\right]^2 e^{-x^2/2}\,dx.$$
By the identity in the original post, this is equal to
$$F^{(k)}(1/2) =(2k)!\binom{n}{k}^2 2^{n} \sqrt{2\pi} (n-k)!.$$
Dividing by $k!$ and simplifying gives us
$$\frac{F^{(k)}(1/2)}{k!} = \sqrt{2\pi}\, 2^{n} n!\,\binom{2k}{k}\binom{n}{k}.$$
These are the coefficients of the expansion of $F$ centered at $a^2 = \tfrac{1}{2}$, so we arrive at
$$\int_{-\infty}^\infty |H_n(ax)|^2e^{-x^2/2}\,dx = F(a^2) = \sqrt{2\pi}\,2^n\,n!\cdot\sum_{k=0}^n \binom{2k}{k}\binom{n}{k}\left(a^2-\tfrac{1}{2}\right)^k.$$