I will present an example involving only (non-compact) manifolds without boundary. As far as I know, the analogous problem for closed manifolds is wide open. Nevertheless, the article Configuration spaces are not homotopy invariant by Paolo Salvatore and Riccardo Longoni is very much worth looking at (it was published in Topology, volume 44, number 2, 2005, pages 375-380).$\newcommand{\RR}{\mathbb{R}}$$\newcommand{\Conf}{\mathrm{Conf}}$$\newcommand{\To}{\longrightarrow}$
Proposition: Assume $n \geq 3$. Let $W$ be a contractible topological $n$-manifold without boundary, and $O \subset W$ an open subspace homeomorphic to $\RR^n$. Then the inclusion of $O$ into $W$ induces homotopy equivalences on all ordered and unordered configuration spaces.
A few consequences of this are:
An embedding $V \to W$ between contractible $n$-manifolds without boundary induces a homotopy equivalence on all ordered and unordered configuration spaces.
If $V$ and $W$ are contractible $n$-manifolds without boundary, then there are homotopy equivalences $\Conf(V,k) \simeq \Conf(W,k)$ between their ordered configuration spaces, and $C_k V \simeq C_k W$ between their unordered configuration spaces.
In particular, the configuration spaces, both ordered and unordered, of the Whitehead manifold are homotopy equivalent to the corresponding configuration spaces of $\RR^3$.
The remainder of this post discusses the proof of the proposition above. Here is a lemma which will be used.
Lemma: Let $S$ be any finite subset of $O$. Then the inclusion $O\setminus S \to W\setminus S$ is a weak equivalence.
Proof:
Apply the van Kampen theorem to the open cover of $W$ by $O$ and $W\setminus S$. Since $O\setminus S$ is simply connected (since it is equivalent to a wedge sum of $(n-1)$-dimensional spheres), it follows that $\Pi_1(W\setminus S) \simeq \Pi_1(W)$ is trivial.
Now apply the Mayer–Vietoris sequence for homology to the same open cover of $W$ by $O$ and $W\setminus S$. The contractibility of $W$ implies that the inclusion $O\setminus S \to W\setminus S$ is a homology equivalence. Since both spaces are simply connected, this inclusion is also a weak equivalence. ■
Now we prove that the map on ordered configuration spaces $\Conf(O,k) \to \Conf(W,k)$ is a weak equivalence for any $k>0$. Note that we have a map of (horizontal) fibration sequences
$$
\begin{matrix}
O\setminus S & \To & \Conf(O,k) & \To & \Conf(O,k-1) \\
\big\downarrow & & \big\downarrow & & \big\downarrow \\
W\setminus S & \To & \Conf(W,k) & \To & \Conf(W,k-1)
\end{matrix}
$$
where $S$ is any subset of $O$ of size $k-1$. The previous lemma states that the map on the fibres is a weak equivalence. Thus, by induction on $k$, we conclude that the map $\Conf(O,k) \to \Conf(W,k)$ is a weak equivalence.
Now the result for unordered configuration spaces follows since we have a commutative diagram of fibration sequences
$$
\begin{matrix}
\Sigma_k & \To & \Conf(O,k) & \To & C_k O \\
\big\downarrow & & \big\downarrow & & \big\downarrow \\
\Sigma_k & \To & \Conf(W,k) & \To & C_k W
\end{matrix}
$$
which is an equivalence on the fibres and total spaces. We conclude that the map on the base spaces is also a weak equivalence.