Not a new cover. Just the OEM cleaned up and painted. Yes, in the first pic the outer nut is just there to hold the washers in place to check for flatness. It comes off, water pump goes on, nut goes back on.
You could put the washers under the first nut. This would probably be fine. This nut doesn't have as much surface area as the washer to support the water pump. This is why I chose nut first, washers second. It's not perfectly flat. It never will be. Every little thing would need to square and/or parallel to one another to make it perfectly flat. This isn't the case. You just do the best you can.
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Stanton
'88 Formula, red on gray