Hello,
To say it in a popular way; there is lots of air between the patches and the ground plane (and in between the patches), so most of the field lines go through air, reducing the influence of the substrate. So you may see a small reduction in center frequency when changing from RT Duroid to FR4. As the design is rather wide band, you may not even notice this. You don't have to worry about your observations.
Small (with respect to wavelength), high gain and wide band don't go together, this is a physical limitation rather then a technical. If you want a smaller antenne, gain and or efficiency will reduce.