We need to condition on the $\sigma$-algebra generated by the stopping time $\tau_U$, instead of $X(t)$.
Preliminaries
Recall the definition of the $\sigma$-algebra of events prior to $\tau_U$:
$$
\mathcal{F}_{\tau_U}:=\{A\in\mathcal{F}\mid A\cap\{\tau_U\le t\}\in\mathcal{F}_t\}.
$$
Note $\{\tau_U\le t\}\in\mathcal{F}_{\tau_U}$.$\renewcommand{\P}{\,\mathbb{P}}\newcommand{\E}{\,\mathbb{E}}
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The strong Markov property can be expressed as:
$$
\E^x[1_{\Brace{\tau_U<\infty}}f(X_{\tau_U+t})|\F_{\tau_U}]=1_{\Brace{\tau_U<\infty}}\E^{X_{\tau_U}}[f(X_t)],
$$
where $f:\R^n\to\R$ is any bounded measurable function. Here, we assume that we don't need to bother with $1_{\Brace{\tau_U<\infty}}$ since $\tau_U$ is finite. To ensure this finiteness, we need additional condition on $\{X_t\}$ in addition to what you described, but no worries.
Answer
First conditioning on $\F_{\tau_U}$, and then using the strong Markov property, we conclude:
\begin{align*}
\P^x[X_t\in A,\tau_U\le t]&=\E^x\SQuare{1_{\Brace{\tau_U\le t}}\E^x[1_{\Brace{X_t\in A}}|\F_{\tau_U}]}\\
&=\E^x\SQuare{1_{\Brace{\tau_U\le t}}\P^{X_{\tau_U}}[X_{t-\tau_U}\in A]}.
\end{align*}
The last expectation can be readily expressed as the following integral. Note that we have two random variables, $\tau_U$ and $X_{\tau_U}$, in the expectation.
\begin{align*}
\int^t_0\int_{U^\complement}\P^z[X_{t-u}\in A]\P^x[\tau_U\in du,X_u\in dz].
\end{align*}
Under additional assumptions, such as $\{X_t\}$ a.s. having continuous sample paths, the inner integral can be taken on $\Gamma$, instead of the entire $\R^n\setminus U$.