Indigenous Taiwanese tribes may be a branch of the ancestors Polynesians are descended from.
The genetic data suggests two possibilities.
The first is that Polynesians are descendants of the Taiwanese tribes.
The second is that the Taiwanese tribes and the Polynesians branched from the same mother stock around the same time, such that the mitochondrial DNA would be indistinguishable between the parent stocks for both branches.
A third, far less probable, possibility is that the genetic similarities between the mitochondrial DNA of both branches occurred separately, and such similarities are merely coincidence... Chances being anywhere from no chance in Hell, to no chance in purgatory, of such a coincidence ever occurring naturally in nature.
You left out the fourth and even far less probable, that both populations are human/alien hybrids, using the same human and alien stock...