This is not like Fallout or some fictional alternative U.S. history.
It definitely is if we for example assume that TFPs White River is the actual White River. You yourself showed that 7d2d does not line up with reality. Or the alternative is true, that the names are just used because they are somewhat familiar names you would or could see on a map of Arizona (Navezgane for example is pure invention, right?).
The "corrupt casino Indian" trope is not a creation of The Fun Pimps. It has been around in modern media for decades. Casino Indians have been portrayed as the "bad guys" in South Park, Family Guy, the Sopranos, Longmire, House of Cards, and many more. (I also mentioned Z Nation, though IMHO that show handles it better, since they weren't the only Native Americans.)
In fact if there are any Native Americans at all in modern American media, it's likely that they will be casino Indians. There are exceptions, but they are exceptions, not the rule.
We also have greedy cooperations, dumb blondes and practically all casino owners as tropes. All negative and commonly used in comedy because you don't need long introductions to set up new characters in it or make jokes about it. The other common use of tropes is in action series, half of them have a greedy cooperation as enemy, together with lawyers, though naturally we can't really hurt the feelings of cooperations (or lawyers

)
But drop the "indian" from "indian casino owner" and you still have almost the same trope. How many movies and series do you know where a casino owner was not doing something illegal or part of the mafia? Compared to the other way round?
Notice that you are freely switching between the "crooked casino indian" and "casino indian" tropes in your description, and only the former would be really problematic. And we also don't know whether the duke was a crooked one when he still owned a casino. I can immediately remember a Mentalist episode with "casino indians" where the culprit was the non-indian head of security.
In fact if there are any Native Americans at all in modern American media, it's likely that they will be casino Indians. There are exceptions, but they are exceptions, not the rule.
It was also satirized in It's Always Sunny In Philadelphia. In a couple episodes, the gang makes fan sequels of Lethal Weapon. The bad guy in the movies is Chief Lazarus (played in-show by Frank, real actor Danny DeVito), who is a corrupt casino Indian that poisons the L.A. water supply. It's clearly a satire of racial stereotypes - these are the same episodes where both Mac and Dennis play Murtaugh by donning blackface, which Frank says is OK if they get the right color of shoe polish.
The Fun Pimps also did not invent the "savage Indian raiders vs. innocent White settlers" trope. That trope has been around as long as America was mythologizing its Western past, from Buffalo Bill's Wild West Show to the Lone Ranger to 20th century Western movies to kids playing "cowboys and Indians."
You do know that 7d2d tries to be humorous or even satirical itself? When satire is not in-your-face (like in "Always.." as far as I know the show) it can be hard to differentiate between using a trope and making fun of it. Best example is "starship troopers", the book as well as the movie. I would assume for most people it is perfectly clear that the society in the movie is satirized, but on release lots of people and reviewers didn't get that.
As we don't know the details of the story we can not even guess here. A lot depends on details or if details exist at all. If the Duke and Noah are just cardboard figures whose names turn up in a few sentences I would call the potential damage minimal, likewise if they are well-rounded characters with positive and negative traits (like The Flu mentioned quite correctly).
And, it is not me calling these tropes negative racial stereotypes. It's sociologists, scholars, and Native Americans themselves. It's not a matter of opinion - denying that they are negative racial stereotypes is just factually incorrect.
I'm not asking for Native Americans to all be "good guys," or that the "bad guys" have to be White. I just don't want these stereotypes to be uncritically incorporated as the main story line in a game I love.
I already gave several scenarios where the Duke could be basically the same character, including being Native American, without needing the "casino Indian" trope (he could be a tribal government leader, chief of police, sheriff, military leader, whatever).
I also would prefer if the game didn't erase all Native Americans from a place they lived in for millennia, seemingly in order to advance an "Indian raiders vs. White settlers" story line.
I really don't think this is very much to ask.
You are asking that they rewrite the story after probably having written it down in detail years ago. I think your warning has some merit, TFP should be reminded that they are handling a hot iron that could potentially do damage, but we can't know whether there is a need for change at all (they could already have had satire in mind for example). And we also know that even if there is need for some change or correction that TFP won't let us decide which change is made that still makes the story work as intended.
I don't know how much that trope is ingrained in US society though, from my point as non-US consumer of lots of hollywood products I am confronted with hundreds of tropes, many of them negative, and many also about race. And if I had to rate them for how problematic they are the casino indian would be very very low on my list and the "crooked casino indian" still quite low. But I am looking from the outside, sure.
PS: I would assume that currently nobody is working at all on story, so it might be useful to mention this as a potential problem again when that time comes.