Re the GH and KH testers - ignore what the instructions say about safe levels. There are no 'safe' levels for GH and KH. Different fish have different GH requirements and what would be safe for a soft water fish is not safe for a hard water fish. KH does not directly impact fish so again there is no safe level. KH indirectly affects fish by stabilising pH. If there is not much of it, pH can drop, which does affect fish.
If the substrate was affecting the pH I would expect the GH and KH in the tank to be different from plain tap water. When substrate increases pH, it is because it is also increasing GH and KH.
If the substrate was affecting the pH I would expect the GH and KH in the tank to be different from plain tap water. When substrate increases pH, it is because it is also increasing GH and KH.