I can see why he might want to make Marlow an American, given that he intended to play him himself, but Marlow has to be in Europe anyway to get his Congo gig. Why couldn't he be telling his tale in London? It would require far less rewriting of Conrad.
The answer is I suppose that Welles wanted to rewrite Conrad. Moving Marlow's telling to Manhattan means that his disquisition on how this too has been "one of the dark places of the earth" now applies to America, not Britain. The evocation of the hard times endured by Roman soldiers is transferred to the earliest European colonists, when "our fathers first came here". (This, according to Marlow, happened "four hundred years ago", which is way out for Manhattan, or indeed for any English colony - but perhaps the Spanish are "our fathers" too for his purposes?) And of course it implies a parallel between the Native Americans and the Africans colonized by the European powers of Marlow's own day, as well as obliquely asserting the nature of America's imperial present and future.
At the very least, it's an interesting choice. But how well does it work? And how convincing is James McAvoy's accent? I'd be interested to hear a transatlantic view on the first five minutes, even if you don't listen to the whole thing.