It cannot be done directly from Synapse settings, but you can do it manually by editing Synapse configuration.

1. Close Synapse
2. Edit ~/.config/synapse/config.json
3. Set activate to Super_L

{
  "ui" : {
    "shortcuts" : {
      "activate" : "Super_L",
      ...
    }
  }
}

There is a disadvantage of this solution. You basically can’t use any other global key combinations with Win key, because it will always trigger Synapse.

If that is a problem you can use xcape to assign an additional one-click function to a modifier key.

xcape -e 'Super_L=Super_L|space'