EDIT: A previous version of this question was imprecisely formulated—I am grateful to Theo Bendit for providing a counterexample for that version.
Let, for some $n\in\mathbb N$, $X\subseteq\mathbb R^n$ be a convex polytope (the convex hull of a non-empty finite set of points) and $(\overline x_1,\ldots,\overline x_n)\in X$. Define $$Y\equiv\{(y_1,\ldots,y_n)\in\mathbb R^n\,|\,y_i\geq\overline x_i\text{ for $i=1,\ldots,n$}\}.$$ Moreover, suppose that the intersection $X\cap Y$ consists of the one and only one point $\{(\overline x_1,\ldots,\overline x_n)\}$.
These conditions ensure that $X$ and $Y$ can be separated by a hyperplane: there exist some $p_1,\ldots,p_n\in\mathbb R$, not all zero, such that $$p\cdot y\geq p\cdot x\quad\text{for every $x\in X$ and $y\in Y$.}\tag{$\diamondsuit$}$$ Moreover, it is not difficult to check that the $p_i$’s are actually non-negative.
My conjecture is that all of the separating hyperplane coefficients can be taken to be strictly positive: it can be arranged in ($\diamondsuit$) that $p_i>0$ for $i=1,\ldots,n$. The goal is to ensure that the resulting hyperplane is “slanted,” as it were (not parallel to any of the axes).
I am 99% sure this conjecture is true, but the details of the proof have eluded me thus far. Any hints would be appreciated.

Let’s add the remaining one percent to the truth assurance.
Let $\overline x=(\overline x_1,\ldots,\overline x_n)$, $K$ be a convex cone spanned by $X-\overline x$, and $$\Bbb R^n_+=Y-\overline x=Y\equiv\{(y_1,\ldots,y_n)\in\mathbb R^n\,|\,y_i\geq 0 \text{ for $i=1,\ldots,n$}\}.$$
Since $X$ is a convex hull of a finite set, the cone $K$ is spanned by a finite set, so, by Weyl’s Theorem, $K$ is polyhedral and therefore closed (see, for instance, [Paf, Theorem 1.8] and Definition 1.3 of a polyhedral cone), and the intersection $K\cap \Bbb R^n_+=\{0\}$ is trivial. Then by Theorem 7 from §30 of [Cha], there exists a vector $p$ satisfying ($\diamondsuit$) with all positive components.
The proof is the following. Let the dual cone $K^*$ consists of all vectors $p\in\Bbb R^n$ such that $px\le 0$ for all $x\in K$. Suppose to the contrary that the cone $K^*$ contains no vectors with all positive components. Pick $a\in \Bbb R^n$ and $b\in\Bbb R$ such that $a\cdot x\ge b$ for each $x\in \Bbb R^n_+$ and $a\cdot x\le b$ for each $x\in K^*$. Since $0\in \Bbb R^n_+$, $a\cdot 0=0\ge b$. So $a\cdot x\le 0$ for each $x\in K^*$, that is $a$ belongs to a dual cone $K^{**}$ of $K^*$. We have $K=K^{**}$ by Theorem 1 from §30 of [Cha] for a closed $K$ or Lemma 1.12.3 in [Paf] for a finitely generated $K$, so $a\in K\setminus\{0\}$ and there exists $a_i<0$. Let $e^i$ in $\Bbb R^n_+$ be a vector whose $i$-th coordinate is $1$ and other coordinates are $0$. Then $a\cdot \lambda e_i=\lambda a_i<b$ for all $\lambda>0$, which is impossible, a contradiction.
References
[Cha] V.S. Charin, Linear transformations and convex sets, Kyiv: Vyshcha shkola, 1978. (in Russian).
[Paf] Andreas Paffenholz, Polyhedral Geometry and Linear Optimization. Summer Semester 2010.