I would guess that Mark Twain saw the passage from the Overland Monthly and hung on to the idea, maybe subconsciously, until he was working on Roughing It. But aside from the idea of floating above the water on a balloon and the clearness of the water, I don't see any resemblance between the two passages. To put it in "Twain-ish" terms, the first is like a lightning bug, the second is like lightning.