The term "general covariance" is another one that sources tend to get sloppy about. There are two possible ways to interpret it:
(1) If I take a particular spacetime geometry, I can pick any coordinate chart I like on that geometry, and write down the metric for that geometry in my chosen chart, and the metric I write down will be a solution of the Einstein Field Equation. The transformation between any two such charts will be a diffeomorphism. Furthermore, when I compute physical invariants, they will be the same regardless of which chart I pick (since the underlying geometry is the same).
(2) If I take a particular solution of the Einstein Field Equation, expressed in a particular chart, I can do a coordinate transformation that changes the metric, but still ends up with a (different) metric that is a solution of the Einstein Field Equation. Any such transformation will also be a diffeomorphism.
The purported transformation from Kruskal to Minkowski coordinates that you refer to would be an example of #2, if it actually existed; however, it doesn't as you state it, at least not as a diffeomorphism, because the underlying topological spaces are different (Kruskal coordinates are on R2 X S2, the underlying manifold of maximally extended Schwarzschild spacetime, while Minkowski coordinates are on R4). (You could restate it as a transformation between a patch of Kruskal/Schwarzschild spacetime and a patch of Minkowski spacetime, and have it be a diffeomorphism.)
I personally don't find transformations of type #2 very interesting, because you're basically changing everything that's of physical interest, so what's the point? But mathematically, they do exist, and "general covariance" can be interpreted as including them, yes.