You are correct clearing the inventory like that will not work anymore as the actual inventory is not stored there anymore. (They are still updated for compatibility). If you want to properly add/remove items from the inventory then you should use $gameParty.gainItem().
I have just updated the plugin, and to help you I also added a plugin command: ClearPlayerInventory
This plugin command will clear the player's inventory. However, if you want to use script then you can now also write: $gamePlayer.clearInventory()