My main question is
Q1. Let $B$ be a Borel-measurable subset of $\mathbb R$. Is there a sequence of open sets $U_n$ independent of any measure such that for all Borel probability measures $\mu$ on $\mathbb R$, $\mu(B \Delta U_n) \to 0$?
Any open set is trivially a measure-independent limit of open sets.
Any closed set is an intersection of a nested sequence of open sets and hence is a measure-independent limit.
I wonder if Q1 can be answered negatively by showing that $\mathbb Q$ is a counter example.
Q1a. Is $\mathbb Q$ a counter example?
If $B$ is a measure-independent limit of $U_n$ then $1_B$ is a pointwise-limit of the sequence $1_{U_n}$ because of Dirac delta measures. Maybe this can be used to show that $\mathbb Q$ is a counter example, but I don't know how.
Motivation: last paragraph of the question in https://mathoverflow.net/questions/167823/the-borel-sigma-algebra-of-the-set-of-probability-measures?rq=1
I can sharpen PhoemueX's very nice answer a little bit. In particular, yes, $\mathbb{Q}$ is a counterexample.
You are quite right that, if a set $B$ is to be the measure-independent limit of a sequence of sets $A_n$, we must have $1_{A_n} \to 1_B$ pointwise. In particular, as PhoemueX says, we must have $B = \bigcup_{k \ge 1} \bigcap_{n \ge k} A_n$. So if $A_n = U_n$ are open then $B$ must be $G_{\delta,\sigma}$.
But we can say more: it must also be that $B = \bigcap_{k \ge 1} \bigcup_{n \ge 1} A_n$. In fact, it is a nice little exercise to show that for any sequence of sets $A_n$, we have $$\limsup_{n \to \infty} 1_{A_n} = 1_{\limsup A_n}, \qquad \liminf_{n \to \infty} 1_{A_n} = 1_{\liminf A_n}$$ where $$\limsup A_n := \bigcap_{k \ge 1} \bigcup_{n \ge k} A_n, \qquad \liminf A_n := \bigcup_{k \ge 1} \bigcap_{n \ge k} A_n.$$ So in particular if $1_B = \lim_{n \to \infty} 1_{A_n}$ pointwise, then we have $1_B = \limsup 1_{A_n} = \liminf 1_{A_n}$ and hence $B = \limsup A_n = \liminf A_n$.
And when $A_n = U_n$ are open, then $\limsup U_n$ is actually $G_\delta$. So in order for a set to be a measure-independent limit of open sets, it must be both $G_\delta$ and $G_{\delta,\sigma}$.
However, $\mathbb{Q}$ is not $G_\delta$. Since $\mathbb{Q}$ is dense, if it were $G_\delta$ it would be a dense $G_\delta$, or in other words comeager. But since $\mathbb{Q}$ is countable it is also meager. This contradicts the Baire category theorem: $\mathbb{R}$ is not meager, so no subset of $\mathbb{R}$ can be simultaneously meager and comeager.