When it comes to general covariance, it covers not only linear(-affine) transformations which make up the group $GL(n)$, but also non-linear transformations. A very basic example of it for instance is the choice of spherical coordinates: $$t = t'$$ $$x = r \sin\theta \cos\phi$$ $$y = r \sin\theta \sin\phi$$ $$z = r \cos \theta$$ Of course the invariant line element no longer looks like a Minkowski-metric, but this is the essence of general covariance, that it deals with any kind of metric. $$ds^2 = dt'^2 -dr^2 -r^2(d\theta^2 + \sin^2(\theta) d\phi^2)$$ (Of course linear coordinate transformations which are not Poincare' can also already change the metric --- for instance $u=t+r$ and $v=t-r$). The given example of course does not change the property of the given space being flat. Actually a flat space cannot be become curved by a general coordinate transformation.