Too lazy to do my own research, but I'm not sure that stuff really supports that enemy combatants can be detained indefinitely, and it definitely doesn't indicate that those people are held in US prisons.
It looks like the S.C. case that held Padilla could not file for Habeas was never challenged because he was actually indicted soon after. The article you pasted at the end was written in 2004, before a lot of this stuff really got tested in court.
At best, it's an open issue, but it's one that I guarantee the Pres does not want to deal with on US soil.