This is based on Anonymous answer.
Theorem. Let $X_0$ be a strongly zero-dimensional Tychonoff space, $Y\subseteq \beta X_0\setminus X_0$ a locally compact scattered space. Then $X = \beta X_0\setminus Y$ is such that $\beta X\setminus X = Y$ and $X$ has only zero-dimensional compactifications.
Remark. In Anonymous example, we have $Y = N$ and $X_0 = \mathbb{N}$, and all the assumptions hold. Clearly $Y$ is compact iff $X$ is locally compact.
Proof:
Suppose $K$ is a compactification of $X$ and let $S\subseteq K$ be a compact connected set with more than two points. Note that $\beta X = \beta X_0$ since $X_0\subseteq X \subseteq \beta X_0$ and so there exists a surjective map $\beta X_0\to K$ which maps $X$ to itself and $Y$ to $K\setminus X$.
Since $\beta X_0\setminus \text{cl}_{\beta X_0} Y \subseteq K$ is open, given $p\in S \cap (\beta X_0\setminus \text{cl}_{\beta X_0} Y)$ and $q\in S, q\neq p$, there exists a clopen compact subset $U$ of $\beta X_0\setminus \text{cl}_{\beta X_0} Y$ with $p\in U, q\notin U$, which is impossible. So that we need to have $S\subseteq \text{cl}_{\beta X_0} Y \setminus Y\cup K\setminus X$. Let $L = \text{cl}_{\beta X_0} Y \setminus Y\cup K\setminus X$, $L$ compact.
Since $Y$ is locally compact, $\text{cl}_{\beta X_0} Y \setminus Y$ is closed in $L$, so $K\setminus X$ is open in $L$. The map $Y\to K\setminus X$ is perfect and so by this answer by K. P. Hart, $K\setminus X$ is open and zero-dimensional. If now $p\in S\cap (K\setminus X)$ and $q\in S, p\neq q$, then we can take a clopen compact subset $U$ of $L$ with $p\in U, q\notin U$, so as previously we can assume $S\subseteq \text{cl}_{\beta X_0} Y \setminus Y$.
Since $\text{cl}_{\beta X_0} Y \setminus Y$ is subspace of zero-dimensional space, it's itself zero-dimensional. And so there can't be a connected $S\subseteq \text{cl}_{\beta X_0} Y \setminus Y$ with more than two points.
It follows that $K$ is totally disconnected and compact, and so zero-dimensional. $\square$
Example. If $Y$ is a strongly zero-dimensional, locally compact, scattered space, then there exists a space $X$ with only zero-dimensional compactifications and $\beta X\setminus X\cong Y$.
Proof: Let $\alpha > 0$ be a non-limit ordinal with $|\beta Y| < \aleph_\alpha$ and $X_0 = \beta Y\times \omega_\alpha$. Then $\beta X_0 = \beta Y \times (\omega_\alpha + 1)$ is zero-dimensional. The space $X = \beta X_0\setminus (Y\times \{\omega_\alpha\})$ has only zero-dimensional compactifications and is such that $\beta X\setminus X \cong Y$. $\square$
Corollary. Let $X$ be a strongly zero-dimensional Tychonoff space with $\beta X\setminus X$ locally compact. Then the following are equivalent:
$X$ has only zero-dimensional compactifications.
$\beta X\setminus X$ is scattered.
Proof: 2 implies 1 from the theorem.
Suppose $X$ has only zero-dimensional compactifications. Then $\beta X\setminus X$ is zero-dimensional as a subspace of $\beta X$. If $\beta X\setminus X$ weren't scattered, then we would find a compact perfect set $A\subseteq \beta X\setminus X$ as in K. P. Hart answer and so there would exist a surjection $A\to [0, 1]$. Since $\beta X\setminus A$ is locally compact, from Engelking theorem 3.5.13 there exists a compactification $Z$ of $\beta X\setminus A$ with remainder homeomorphic to $[0, 1]$. Its also a compactification of $X$, and $Z$ is not zero-dimensional. The contradiction shows that such set $A$ cannot exist, and so $\beta X\setminus X$ is scattered. $\square$