So basically, now, the U.S. government is saying that it has identified the thief of Indian royalties and resources as itself. It has allowed the thief to determine the value of the settlement and mostly has allowed the thief to keep what has been stolen.
However, the question is not who pays the bills of a Federal judge, but where the incentives for the judge lie. Evidence that there is a principal-agent "problem" for the Federal judge that decided the case is exiguous. Just because the salaries of judges are paid by the federal government does not mean that they are beholden to it. In this case, a judge has little reason to rule "for" or "against" the government, as he gains nothing from either outcome. It is ludicrous to claim shadowy conspiracy without first asking "what are the incentives of relevant actors?"