What I'm not clear on is how hard and fast the rules of usage were - as you can see here, the uniform patch has the eagle looking to its left, but the helmet decal has the eagle looking to its right.
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BUT, International Military Antiques has a reproduction paint stencil and this is their description:
'IMA has developed an accurate stencil of the Infamous Nazi Eagle over Swastika known as "The Reichsadler". This symbol during the time of Nazi rule represented Nazi Germany as a national insignia. It was painted extensively on Ammunition boxes, Wooden Crates, Transport Containers, and anything the Germans wanted identified as official property of the Third Reich.'
So, based on that I would maintain that the eagle on the Ark crate is in fact correct.