Literally just added + this.helpAreaHeight() to line 1868:
var wy = (Utils.RPGMAKER_NAME == "MV") ? this._helpWindow.height : (this._buttonAssistWindow && this.buttonAssistWindowRect().y > 100) ? 0 : this.buttonAreaHeight()
Changing it into:
var wy = (Utils.RPGMAKER_NAME == "MV") ? this._helpWindow.height : (this._buttonAssistWindow && this.buttonAssistWindowRect().y > 100) ? 0 : this.buttonAreaHeight() + this.helpAreaHeight()