The opinion in that case seems to be that Indian nations are sovereign and so an Indian born within an Indian nation is a citizen of that nation and not the US. This doesn't seem to be incompatible with the 14th Ammendment which mentions representation apportioned by whole persons, excluding Indians not taxed. US Citizenship of tribal members was also part of treaties between the US and the tribes.
That situation doesn't arise other than with Indians, because the US does not enter into treaties with any other groups formed within the boundaries of the US. Although the 1871 Indian Appropriation Act prohibited new treaties with Indian nations.
This seems fairly simple; we made treaties with Native American tribes, up until 1871, and Article I says things like "excluding Indians" and "regulate Commerce with foreign nations and among the several states, and with the Indian tribes".
They clearly enjoy special (so to speak) status from day one.
Let me put it this way. What is a definition of “subject to the jurisdiction” that excludes Indians, other than saying “well, Indians aren’t included?” It can’t be “people who aren’t subject to US laws,” because Indians have been subject to U.S. laws since 1817, even on tribal lands.