Since $X_1$ and $X_2$ always show up together in the OP, I will just use $X$ to denote them. Also, the terms "correlation" and "covariance" are used casually in the OP. I'll specifically study "covariance" here.
The covariance part in $\eta^2$ is
$$\newcommand{\C}{\mathbb{C}\mathrm{ov}} \newcommand{\V}{\mathbb{V}\mathrm{ar}} \newcommand{\E}{\mathbb{E}} \begin{align}
&\phantom{{}={}} \C\left\lbrace D-\E(D\mid X),\quad \E\left[D-\E(D\mid X) \mid X,Z \right] \right\rbrace
\\
&=\C\left\lbrace D-\E(D\mid X), \quad \E(D\mid X,Z)-\E(D\mid X) \right\rbrace \\
&=\C\left\lbrace D-\E(D\mid X), \quad \E(D\mid X,Z)\right\rbrace - \\
&\qquad\qquad \underset{0}{\underbrace{ \C\left\lbrace D-\E(D\mid X), \quad \E(D\mid X,)\right\rbrace }} \\
&=\E\left \lbrace
\C\left[D-\E(D\mid X),\quad \E(D\mid X,Z)\mid X\right] \right\rbrace + \\
&\qquad\qquad
\C\left( \underset{0}{\underbrace{ \E\left[D-\E(D\mid X) \mid X\right] }},\quad \E\left[\E(D\mid X,Z)\mid X\right] \right)
\\
&=\E\left\lbrace \C\left[D,\quad \E(D\mid X,Z)\mid X\right] - \right. \\
&\qquad\qquad \underset{0}{\underbrace{ \C\left[\E(D\mid X), \quad\E(D\mid X,Z)\mid X\right] }} \rbrace\\
&=\E\left\lbrace \C\left[D,\quad \E(D\mid X,Z)\mid X\right] \right\rbrace \tag{1}\label{1} \\
&=\E\left\lbrace \underset{0}{\underbrace{\C\left[D-\E(D\mid X,Z),\quad \E(D\mid X,Z)\mid X\right]}} + \V\left[ \E(D\mid X,Z) \mid X \right]
\right\rbrace \\
&=\E\left\lbrace \V\left[ \E(D\mid X,Z) \mid X \right]
\right\rbrace \\
&\geq 0.
\end{align}$$
So, even without squaring, this covariance is already non-negative. Compare \eqref{1} with the (not necessarily non-negative)
$$
\C(D,\ Z)=\E\left\lbrace \C(D,\quad Z\mid X)\right\rbrace + \C\left[\E(D\mid X), \quad\E(Z\mid X)\right].
$$
Apart from the extra second term in $\C(D,\ Z)$, it seems more interesting to me to compare the square of terms inside their first braces:
$$
\left\lbrace\begin{array}{ccc}
\C^2 [\,D, & \E(D\mid X,Z) & {}\mid X\,] \\
\C^2 [\,D, & Z & {}\mid X\,]\\
\end{array}\right.$$
I intuitively think that the upper line will have a larger value, because $\E(D\mid X,Z)$ (as a function of $Z$) is made specifically to approximate $D$, compared with $Z$ itself.
We can also rewrite $\C(D,\ Z \mid X)$ as
$$\begin{align}
\C(D,\ Z \mid X)
&=\E\left[\underset{0}{\underbrace{\C(D,\ Z\mid X,Z)}} \mid X\right]+\C\left[\E(D|X,Z),\ \E(Z\mid X,Z) \mid X\right] \\
&=\C\left[Z,\ \E(D|X,Z) \mid X\right].
\end{align}$$
This provides another comparison with \eqref{1}:
$$\left\lbrace\begin{array}{ccc}
\C [\,D, & \E(D\mid X,Z) & {}\mid X\,] \\
\C [\,Z, & \E(D\mid X,Z) & {}\mid X\,]\\
\end{array}\right.$$