For most purposes, race is not properly a factor to be considered in legal proceedings. In parental rights cases, however, under the Indian Child Welfare Act, a federal law, a child's ethnicity not only may, but must be considered and impacts who has standing in the case and what burden of proof applies in termination of parental rights proceedings.
The Indian Child Welfare Act is not new, and presumably, challenges to it under the 14th Amendment have been attempted and failed.
This isn't the only situation where distinctions are made on ethnic status that would otherwise be improper is permitted when Native Americans are distinguished.
Dead bodies are treated differently if believed to be of Native American descent, Hawaii has a trust that benefits descendants of Native Hawaiians that might not otherwise be valid, and there are certain kinds of hunting and animal parts (whales and bald eagles, for example) that are permitted in a Native American context, likewise peyote can be used for Native American religious purposes where it wouldn't otherwise be allowed. This list is not exhaustive.
One justification for these acts is that they flow from a form of current nationality, a distinction which is proper not only for immigration purposes, but also for treaty purposes. Indeed, the U.S. Constitution, with its "Indians not taxed" clause has long recognized a different status for Native Americans some of the time. Foreign nationals sometimes have different rights, which the federal government may establish.
This justification seems thinner over time, as Native American tribe members have increasingly integrated into the general melting pot of American society. Treaties notwithstanding, in daily life, Indian tribes look less and less like sovereign nations. Liechtenstein and the Vatican have more elements of sovereignty. In particular, Indian tribes have the secondary kind of sovereignty associated with U.S. states and federal political divisions, rather than the absolute sovereignty associated with truly independent states. Indeed, Indian tribe governmental structures in most cases have the lesser sort of independence associated with territorial governments and municipalities within U.S. states, rather than the significant autonomy of U.S. states.
Another justification is that the distinctions made represent different activities. This argument suggests that the real life relationship between the community represented by a tribe and a parent is different that the real life relationship between non-Indians and their communities. Indian tribes might, for example, have a relationship collectively with an Indian tribe, morally equivalent to a grandparent's relationship with a grandchild in much of the rest of U.S. society. In tribes with their own living languages, language issues that cannot be addressed outside a tribe, may be relevant.
Similarly, supervised religious drug use may differ from recreational drug use in the rest of society, and while it might be theoretically possible that other groups have bona fide religious drug use, legislators may not be convinced in reality there are other such bona fide users out there.
A third justification, at least in the child custody area, might be that this is a form of affirmative action in response to a history of abuse by courts in this area in the past, based upon the conclusion that this history is proof of a greater risk of abuse in the future by the courts. Child custody is particularly prone to this risk because it makes judgments on parenting based upon largely uncodified cultural parenting norms of the judge, the jury and social services agencies.
I don't know the cases in Indian law very well, or the actual justifications that are the basis for existing law. Likewise, I'm not terribly worried about the exceptions. The percentage of cases, and the number of people, respectively, that are impacted is modest outside a very small number of jurisdictions near Indian reservations. The definition of Indian tribe membership, moreover, which is based upon how many ancestors of a certain degree one has from a tribe (which varies from tribe to tribe), prevent these special rules from ballooning in importance.
Further, the select legal privileges afforded Indian reservations seem, on the whole, to be outweighed by the miserable state of law enforcement, weak economic situations, and limited government services that exist on most of those reservations. And, many of these legal distinctions are distinct to matters on or related to aactivities that are based at reservations.
Perhaps the most interesting question about Indian law is whether it is constitutionally unique. Can one constitutionally have, for example, different family law rules for members of different cultures, as many countries do now and as Britain is considering doing.
In the case of polygamy, the courts have generally said no. In the case of cousin marriage and of the formalities of marriage (including common law marriage) divergent practice has been generally tolerated. Courts have been skeptical, but not completely dismissive, of rabinnical arbitration in family law cases. Perhaps most notably, courts have generally taken a mixed approach to community property rights, honoring community property rights that accrue while a couple live in a community propety jurisdiction, while applying their own laws to other time periods.
Also, even if distictions can be made, should they be made? Have the distinctions made between Indians and non-Indians in American law been a success? Are Native Americans collectively and individually better off as a result? Is the United States more honorable as a result? Has anyone been harmed by these rules, and if so, whom? Has the Indian Child Welfare Act been a net benefit to Indian children, for example?
The Indian Child Welfare Act is also a natural social experiment that couldn't otherwise be ethically conducted that tests whether stronger protections for parental rights have any meaningful impacts for good or ill.