I tried setting AutoGenerateDeleteColumn to True with scrolling enabled at my end, but could not replicate your issue. Check out for the following points.
In order to display horizontal scroll for navigation, you need to make sure that the total width of the columns (either auto-generated or declaratively set) exceeds the width of the grid. Also, set the scroll height to display vertical scroll.
You can swap columns as shown below to change the positions of columns.
| protected void RadGrid1_PreRender(object sender, EventArgs e)
| RadGrid1.MasterTableView.SwapColumns("FirstColumn", "AutoGeneratedDeleteColumn");