In your example,
\begin{align*}
\frac{y_2 - y_1}{x_2 - x_1} &= {8-3}{5-3} = \frac{5}{2} \\
\frac{y_1 - y_2}{x_1 - x_2} &= {3-8}{3-5} = \frac{-5}{-2} = \frac{5}{2} \\
\end{align*}
So it's not really the arctan that's obscuring the order of the points, it's the slope formula.
In the general formula:
$$
\tan \theta = m = \frac{y_2-y_1}{x_2-x_1}
$$
$\theta$ is the angle measured from the positive $x$-axis to the line with slope $y=mx$. Since $m$ doesn't depend on the order of the points, $\theta$ won't either, not from this formula.
If you want an orientation-dependent vector angle formula in $\mathbb{R}^2$, you can use the cross product. If $\vec u = \left<x_1,y_1\right>$ and $\vec v = \left<x_2,y_2\right>$, then $\vec u \times \vec v = \left<0,0,x_1y_2 - x_2 y_1\right>$ will have a positive $z$-component if $\vec v$ is counterclockwise from $\vec u$, and negative if clockwise. Indeed,
$$
\sin\theta = \frac{x_1y_2 - x_2y_1}{\sqrt{x_1^2 + y_1^2} \sqrt{x_2^2 + y_2^2}}
$$