In the long run, separate countries in one system does not really work (and yes, the states and feds are overlapping jurisdictions), but Indians have a much more special status under the law. Race based preferences never end well, even if they seem nice to begin with.
Why? Because it is scary that you can actually have governments make laws that Americans may become subject to when those governments have very few duties under American law to respect American rights. Of course, we do not expect other countries to follow American law, but reservations are not set up as other countries. Moreover, the law is strange in that a tribal member in a part of Oklahoma is now due special criminal treatment due to their ancestry, rather than be subject to the laws of Oklahoma.
That is not okay. Either a border needs to be set up, or the tribal governments need to be cast aside or at least become subject to the same kinds of restrictions the states are. Yes, this will require a constitutional amendment, but frankly, special treatment of Native Americans is a relic of a bygone era, much like slavery.