The derivation of Gauss electric flux is as follows :
$$\iint{\vec{E}}\cdot{\vec{dS}}=\iint E \, dS \cos\theta \, .$$
The projection of infinitesimal area on the surface $\vec{dS}$ on the radial direction of electric field $\vec{E}$ (i.e. $dS \cos\theta$) is equal to the element area of sphere $r^2 (\sin \varphi) \, d\varphi d\phi$.
Therefore, \begin{align} \iint{\vec{E}}\cdot{\vec{dS}} &=\iint\frac{1}{4\pi\epsilon_0} \frac{q}{r^2}(r^2 (\sin\varphi) \, d\varphi \, d\phi) \\ &=\dfrac{q}{4\pi\epsilon_0}\iint(\sin\varphi) \, d\varphi \, d\phi \\ &=\dfrac{q}{4\pi\epsilon_0}4\pi \\ &=\dfrac{q}{\epsilon_0} \, . \end{align}
Now coming back to the main question:
Electric field at all points on the Gaussian surface is independent of the coordinate system. Also the angle between electric field and area vector on the Gaussian surface is independent of the coordinate system.
However, the infinitesimal area on the surface is not the same in all coordinate systems. For example, in a re-scaled orthogonal coordinate system where $\hat{i}\neq\hat{j}$, then $dx\neq\ dy$ and thus $dS'=dx\ dy$ won't be the same as $dS$ in Cartesian coordinate system. Then will $dS \cos\theta$ be equal to element area of sphere? If so, why?
Will we get a result other than $q/\epsilon_0$ in the other coordinate systems or will we get the same result ($q/\epsilon_0$)?