You can animate the Visibility parameter dial for the figure as well.

As for the many mat issue; that is why i suggested VSS or EZskin to mass apply the non-reactive texture across any or all the figures material zones. This allows for a simple mat to be saved as a preset to be used on any figure or prop as necessary irregardless of the mats or maps used in the original textures. Both are free and can be non-destructive to existing materials changing only the surface parameters and not the maps.

If you want to do body part replacement then we are talking a different solution but for making parts or props disappear I find animated materials invaluable and there is no CR2 hacking necessary.

Are you wanting to make a dial to turn parts on and off? That would require cutting into the CR2 as would a geometry switch.