Does this now apply to all POWs taken captive in future conflicts?
I'm not a lawyer, but this is my take.
This mess is driven in part because the parties in question were not granted POW status, so they did not fall under the protections/restrictions of Geneva Conventions III.
As a signatory to GCIII, GCIII usurps the Constitution (Treaties trump the Constitution in the structure of U.S. law).
Given that, a POW under GCIII can be detained until hostilities end. Then they must be repatriated. If a POW is tried as a war criminal, it must occur within three months of initial capture, and GCIII spells out the rights of the accused.
So I would interpret this to mean the only time a POW could sue for habeas corpus is after the end of hostilities, especially if repatriation is delayed due to negotiation between warring parties.