The probability distribution of $X$ was calculated in Random-matrix theory of thermal conduction in superconducting quantum dots. In the context of that physics problem, the $k\times k$ upper-left submatrix $X$ of an $n\times n$ orthogonal matrix $O$ is the reflection matrix of a superconducting quantum dot with $k$ modes in one opening and $n-k$ modes in the other opening. Such a system is described by the circular real ensemble (CRE) of random-matrix theory.
The probability distribution of $X$ is conveniently described in the singular value decomposition $X=O_1 {\rm diag}\,(x_1,x_2,\ldots x_k)O_2$, where $x_i\geq 0$ are the singular values and $O_1,O_2$ are orthogonal matrices.
The matrices $O_1,O_2$ are independently drawn from $O(k)$ with the Haar measure. The singular values $x_i$ of $X$ are related to the transmission probabilities $T_i$ by $T_i=1-x_i^2$. For $N=\min(k,n-k)$ there is a set $\{T_1, T_2,\ldots T_N\}$ of nonzero transmission probabilities that have the probability distribution
$$P(\{T_1,T_2,\ldots T_N\})\propto \prod_i T_i^{|n/2-k|-1/2}(1-T_i)^{-1/2}\prod_{j<\ell}|T_\ell-T_j|.$$
See equation (5) in the cited paper, with $\beta=1$ and $\gamma=-1$.
Equivalently, in terms of the $x_i$'s themselves, there is a set $\{x_1, x_2,\ldots x_N\}$ of singular values that are strictly smaller than unity in absolute value, with probability distribution
$$P(\{x_1,x_2,\ldots x_N\})\propto \prod_i (1-x_i^2)^{|n/2-k|-1/2}\prod_{j<\ell}|x_\ell^2-x_j^2|.$$
The probability distribution of the matrix elements of the matrix $X$ can indeed be written (for $k<n/2$) as $P(\{X_{ij}\})\propto {\rm Det}\,(1-XX^\top)^{n/2-k-1/2}$, as in the OP. Equivalently, in terms of the symmetric matrix $H=XX^\top$ one has $P(\{H_{ij}\})\propto {\rm Det}\,H^{-1/2}\,{\rm Det}\,(1-H)^{n/2-k-1/2}$.
The OP also asks for the significance of the appearance of the characteristic polynomial ${\rm Det}(1-XX^\top)$. This is easiest to understand for $k>n/2$, when $XX^T$ has $k-n/2$ eigenvalues pinned at unity. These repel the $n/2$ other eigenvalues with a term $\prod_{i=1}^{n/2}(1-x_i^2)^{k-n/2}$.