We will write $P:= \mu$ (for more probabilistic notation) and we will show that $\lim_{n \to \infty} P(U_{\epsilon}) = 1$.
Lemma 1: For all $\epsilon>0$ there exists some $\delta>0$ such that if $(x^1,...,x^k) \in \prod_1^k S^n$ then $\sum_{i
Proof: This is a consequence of the Gram-Schmidt orthogonalization process. Specifically, we define $u^1:=x^1$, then $u^2:=x^2-\frac{\langle x^2,u^1\rangle}{|u^1|^2} u^1$, then $u^3=x^3 - \frac{\langle x^3,u^2\rangle}{|u^2|^2} u^2- \frac{\langle x^3, u^1 \rangle}{|u^1|^2} u^1$, and so on. Then let $e^i:=u^i/|u^i|$, so the $e^i$ form an orthonormal set which was constructed from the original $x^i$ using formulas which depend only on the values of the inner products $\langle x^i,x^j \rangle$. By carefully keeping track and using induction, one may show that $|x^j - u^j|$ (and thus $|x^j-e^j|$) can be made arbitrarily small by making the $|\langle x^i,x^j \rangle|$ very small. $\Box$
Lemma 2: If $U,V$ are independent and uniformly distributed on $S^{n-1}$ then $P(|\langle U, V \rangle|>\epsilon) \leq \frac{1}{n\epsilon^2}$
Proof: By conditioning on $V$ and using independence we may write $$P(|\langle U, V \rangle|>\epsilon) = \Bbb E\bigg[ P\big(|\langle U, V \rangle|>\epsilon \;\big| \;V\big)\bigg] = \int_{S^n} P(|\langle U, v \rangle|>\epsilon)\;\sigma(dv) = P(|\langle U, e_1 \rangle|>\epsilon)$$ where $\sigma$ is the uniform measure on $S^n$, and $e_1=(1,0,...,0)$. The final equality follows by rotational invariance of $\sigma$. Writing $U=(U_1,...,U_n)$ we see that the $U_j$ are identically distributed and $\sum U_j^2=1$. Thus $1 = E[\sum U_j^2] = nE[U_1^2]$, so that $E[U_1^2]=1/n$. Consequently, $$P(|\langle U, e_1 \rangle|>\epsilon) = P(|U_1|>\epsilon) \leq \frac{E[U_1^2]}{\epsilon^2} = \frac{1}{n\epsilon^2}$$ At the end we have used Chebyshev's inequality with the second moment. $\Box$
Proof of the original claim: By combining the two lemmas, we see that $$P(U_{\epsilon}^c) = P\big( d(\{X^1,...,X^k\}, \mathcal O)>\epsilon\big) \leq P \bigg( \sum_{i \delta \bigg) $$$$\leq \sum_{i \frac{\delta}{k(k-1)}\bigg) \leq\frac{k^3(k-1)^3}{n \delta^2} \stackrel{n\to \infty}{\longrightarrow} 0$$
Remarks: it was essential that $k$ is fixed here (though the final line shows that $k$ is allowed to depend on $n$, so long as it grows slowly enough). Also note that we only used pairwise independence in this argument (full mutual independence was not needed).