Remember this was made in 1942
Just a guess here, but an explanation for changes in topography may be: “Though subject to wartime censorship and somewhat misleading in its focus... there is dramatic combat footage shot by Ford himself during the Japanese preliminary bombing raid on Midway Island.”
https://books.google.com/books?id=Oe4AOVHkJ9oC&pg=PA236&lpg=PA236&dq=is+it+true+Filming+of+Midway+with+heston+was+being+done+when+Japan+bombers+came&source=bl&ots=XdnvXJzuAk&sig=9tvQMvitrWT9KXjnlESZqLYblWo&hl=en&sa=X&ei=S1prVaYRi6iDBO32g9gJ&ved=0CEMQ6AEwBQ#v=onepage&q=is%20it%20true%20Filming%20of%20Midway%20with%20heston%20was%20being%20done%20when%20Japan%20bombers%20came&f=false
Something forgotten in all this was that part of the battle of Midway was a Japanese diversionary attack on the Aleutians. The footage showing an island of more substantial height than Midway could have been Attu or Kiska