Regarding your first question: Did Twain simply alter the story to make
it the white Noakes who hangs? My guess is that you're right.
If I may mount one of my pet soapboxes, I think one BIG problem with
too many of us who do literary research is that we don't allow
nearly enough for creativity. We mouth the word a lot....but then we
turn right around and assume everything a writer says must have its
"sources" or "influences."
I'm very fond of a line Gore Vidal once threw at the critics: "I'm a
writer. I MAKE THINGS UP!!"
Twain of course joked constantly about his own lying and inventiveness.
And speaking of ROUGHING IT, another example of his alterations is the
way the story of the old ram changed over the decades.
Good luck with your work.