Actually - the point of variations is to save state of widgets that you have connected to your plugins, not the entire plugin states.
Having said that - there is an option called “Ignore Variations” for each widget that you have. When you enable it - that widget will not be recalled or changed when you change variations so if you mute the “synth” sound for example using a widget that ignores variations - it will stay muted even if you switch between variations.
Hope this helps.