As @pianopaul mentioned, using Setlist mode is the only way to have the variations reset to their original saved state.
But confirming - do you really want the wah to change to set values via variations?
If you use the ‘Follow Hardware’ open in the MIDI tab of the widget properties, your wah widget will always remain linked with your physical pedal position (even across rackspaces if you use the wah in more than one). This has the benefit of you always having confidence what the wah will be set to, as it always follows the actual hardware position.