是被这句控制的
Scene_ItemBase.prototype.showSubWindow = function(window) {
    window.x = this.isCursorLeft() ? Graphics.boxWidth - window.width : 0;
    window.show();
    window.activate();
};


那么咱们可以写个插件, 判定了当前场景跟当前窗口后, 更改其xy位置
(function() {
    var _Scene_ItemBase_showSubWindow = Scene_ItemBase.prototype.showSubWindow;
    Scene_ItemBase.prototype.showSubWindow = function(window) {
        _Scene_ItemBase_showSubWindow.call(this);
        if (this instanceof Scene_Item && window instanceof Window_MenuActor) {
            window.x = 100;
            window.y = 100;
        };
    };
}());

y轴没变化的原因：
Scene_Item.prototype.createCategoryWindow = function() {
    this._categoryWindow = new Window_ItemCategory();
    this._categoryWindow.setHelpWindow(this._helpWindow);
    this._categoryWindow.y = this._helpWindow.height;
    this._categoryWindow.setHandler('ok',     this.onCategoryOk.bind(this));
    this._categoryWindow.setHandler('cancel', this.popScene.bind(this));
    this.addWindow(this._categoryWindow);
};

窗口宽度在下一段
Window_ItemCategory.prototype.windowWidth = function() {
    return Graphics.boxWidth;
};

窗口高度在父类
Window_HorzCommand.prototype.numVisibleRows = function() {
    return 1;
};
再父类
Window_Command.prototype.windowHeight = function() {
    return this.fittingHeight(this.numVisibleRows());
};