The answer is positive if and only if $\mathbb{A}^1\setminus S$ is an arithmetic curve, i.e., $\pi_1(\mathbb{A}^1\setminus S)\subset \mathrm{Aut}(\mathbb{H}) = PSL_2(\mathbb{R})$ is an arithmetic subgroup.
This however does not happen "very often". Let me be more precise.
Note that the Euler characteristic of $\mathbb{A}^1\setminus S$ equals $1-\# S$.
For any fixed integer $e$, there are only finitely many isomorphism classes of arithmetic curves $X$ with Euler characteristic $e$ by Takeuchi's theorem; see Theorem 2.1 in https://projecteuclid.org/download/pdf_1/euclid.jmsj/1230396454
Thus, if you fix an integer $n$, there are only finitely many $\mathbb{A}^1\setminus S$ with $\# S = n$ which share a common finite etale cover with $\mathbb{A}^1\setminus \{0,1\}$.
In characteristic $p>0$, the answer is positive (over any field $k$). Indeed, let $k$ be a field of characteristic $p>0$. Then, by Prop. 5.2 in Achinger's paper Wild ramification and $K(\pi,1)$-spaces, $\mathbb{A}^1_k\setminus S$ is a finite etale cover of $\mathbb{A}^1_k$. Let $f:\mathbb{A}^1_k\setminus S \to \mathbb{A}^1_k$ and $g:\mathbb{A}^1_k\setminus\{0,1\} \to \mathbb{A}^1_k$ be finite etale maps. Now define $X$ to be (a connected component of) the fibre product $\mathbb{A}^1_k\setminus S\times_{f,\mathbb{A}^1_k,g} \mathbb{A}^1_k\setminus\{0,1\}$. This comes with finite etale maps to $\mathbb{A}^1_k\setminus S$ and $\mathbb{A}^1_k\setminus \{0,1\}$.