My view is that these two things aren't unrelated facts. Rather, they're inextricably linked. Twain didn't have a whole novel in mind, he had a one-note joke at Cooper's expense. He wanted everyone to know his racist views so he put them in the form of a Huck and Tom story. Once he told the joke, he lost interest in the project. Spoofing Cooper was the whole point of it.
Here's a brief recap of Twain's unfinished novel:
Tom says he wants to go west and have an adventure among the Indians. Jim is afraid, saying the Indians will "skin" them. Tom launches into a lengthy defense of Indians, extolling their courage, morality, and nobility.
It's the kind of praise you'd see in a "politically correct," feel-good guide to Indians. Or in George Catlin's Creed about Indians. Except Catlin the painter actually visited 48 tribes in the 1830s and knew them from personal experience, unlike Twain.
Anyway, Tom convinces Huck and Jim to head west. They join the Mills family: two parents, three boys, and two girls in one wagon. On the plains the travelers meet Blue Fox and four other Sioux Indians. They camp together for four days.
The Indians are friendly, hospitable, and charming. They talk, hunt, dance, and play games with the travelers. On the fourth day, they inexplicably turn into evildoers. They viciously slaughter the Mills parents and boys and mutilate their bodies. They take the girls and Jim captive; only Huck and Tom escape.
Why'd they do it?
Brace Johnson, the heroic sweetheart of the captured Peggy Mills, arrives to save the day. Johnson ponders the Indians' inexplicable behavior:
More to the point, I've read many accounts of massacres. I've never heard anything like this one. Yes, sometimes Indians and white men met to parlay or trade and one side or the other violated the truce and massacred the other. But after four days of putting on a perfect show of being friendly? I don't think so. I'm guessing no such massacre ever occurred--that Twain made it up in his own bigoted imagination.
Did five adult Indians really have to worry about one old man, three boys who had barely reached manhood, an ex-slave without fighting skills, and a few women and children? I'd say they had the advantage already.
They could've surprised and killed the travelers at any time. Waiting four days didn't guarantee that everything would go right. Rather, it offered numerous chances for something to go wrong. Massacring the travelers at the first good opportunity would've been the smart thing to do.
In short, Twain's scenario doesn't make sense. It doesn't match any Indian behavior I ever heard of. It existed solely so Twain could paint his racist picture of Indians as devils.
Book Indians aren't real Indians?
Finally, Huck gives us Twain's punchlines:
He give me a look that showed me I had hit him hard, very hard, and so I wished I hadn't said the words. He turned away his head, and after about a minute he said "Cooper's novels," and didn't say anything more, and I didn't say anything more, and so that changed the subject.
Even the choice of language confirms Twain's views. In a book they're called "Indians." In reality they're filthy "Injuns." "Indians" is too good a word for them.
Eight and half paragraphs after telling us book Indians aren't real Indians, Twain stopped writing. He'd made his point; he had nothing left to say. He didn't want to share more adventures of Huck and Tom, he wanted to "massacre" the reputation of Indians. Once he got that out of his system, he gave up.
For more on the subject, see Why Not Rewrite Twain's Books? and New Huck Finn Eliminates "Injun."
Below: A Twain-style view of Indians.