Isotropic Case
The case $\Sigma=I_d$ is treated. For $z \sim N(0,I_d)$, let $D$ be the distribution of $z$ conditioned on $|z^\top u| \le \theta$. Then, the rows of $Y$ are iid from $D$. It is clear that $D = TN(-\theta,\theta) \oplus N(0,I_{d-1})$, where $TN(-\theta,\theta)$ is the truncated normal distribution on the interval $[-\theta,\theta]$. By universality of MP law, it follows that limiting spectral distribution (LSD) of $S:=Y^\top Y/n = (n'/n)Y^\top Y/n'$ is as if $Y$ were an $n \times n$ random matrix $\sigma_0 X_0$ with iid entries from $N(0,\sigma_0^2)$, where $\sigma_0^2 = n'/n$. This is MP, with variance parameter $\sigma^2$ and scale
$$
\phi' = d/m = (d/n)(n/n') \simeq \phi / \sigma_0^2.
$$
Let $M \subseteq [n]$ be the indices of the rows of $X$ which are actually selected. For any $z \in \mathbb C\setminus \mathbb R_+$. We have
$$
\begin{split}
\mathbb E[\operatorname{tr}S(S - \lambda I)^{-1} \mid M] &\simeq \mathbb E\operatorname{tr} \sigma_0^2S_0(\sigma_0^2S_0 - z I)^{-1} =\mathbb E \operatorname{tr} S_0(S_0 - z' I)^{-1}\\
&\simeq \operatorname{tr}\Sigma(\Sigma - z'I)^{-1} = \frac{d}{1+\kappa'},
\end{split}
$$
where $\Sigma = \sigma_0^2 I$, $\kappa' := \kappa(-z';\phi')$, $\lambda' := \lambda/\sigma_0^2$, and
$$
\kappa(z;\phi) = \frac{z-(\phi-1) + \sqrt{(z-(\phi-1))^2 + 4z}}{2}
$$
Likewise, we have
$$
\begin{split}
\mathbb E[\operatorname{tr}(S -z I)^{-1} \mid M] &\simeq \sigma_0^{-2}\mathbb E\operatorname{tr}(S_0 -z' I)^{-1} \simeq \sigma_0^{-2}\frac{\kappa'}{-z} \operatorname{tr}\Sigma(\Sigma + \kappa' I)^{-1} \\
&\simeq \frac{\kappa'}{-z}\operatorname{tr}(\Sigma + \kappa' I)^{-1} = -\frac{\kappa'}{z}\frac{d}{1+\kappa'}.
\end{split}
$$
We turn to the calculation of $\operatorname{tr} S^k(S-zI)^{-\ell}$ for any $k,\ell \in \mathbb Z$. Observe that
\begin{align}
\mathbb E[\operatorname{tr} S^k(S-z I)^{-\ell} \mid M] \simeq \sigma_0^{2(k-\ell)}\mathbb E\underbrace{\operatorname{tr} S_0^k(S_0-z' I)^{-\ell}}_{\text{use classical RMT here}}.
\end{align}
It remains to take expectations over $n' \sim Bin(n,p)$, where $p = \mathbb P(|z^\top u| \le \theta) = 2\Phi(\theta)-1$, i.e
$$
\mathbb E\operatorname{tr} S^k(S-z I)^{-\ell} = \sum_{n'=0}^n {n \choose n'}p^{n'} (1-p)^{n-n'}\sigma_0^{2(k-\ell)}\mathbb E\operatorname{tr} S_0^k(S_0-z' I)^{-\ell}.
$$
N.B. Curiously, it seems the value of the above sum is close to the value of the summand evaluated at $n' = np$ (maybe there is a statistical mechanical explanation for this ?).