In a prior post surveying the impact of the Senate version of the NDAA bill (currently in conference negotiations), I emphasized that the Feinstein Amendment made clear that the NDAA did not alter, one way or the other, the government's power to detain citizens. That is, the Feinstein Amendment left in place whatever authority the government has or does not have, already, under the 9/18/01 AUMF. That is still my position as to domestic captures. But on reflection I no longer think it is correct as to foreign captures of US citizens.
The Feinstein Amendment was specific to captures in the United States:
Nothing in this section shall be construed to affect existing law or authorities relating to the detention of United States citizens or lawful resident aliens of the United States or any other persons who are captured or arrested in the United States.
As a consequence, my earlier analysis of the interplay between Section 1031 and 1032 of the Senate version of the NDAA--in which I concluded that the explicit exclusion of US citizens from the mandatory detention rule of 1032 implies the inclusion of US citizens in the general grant of detention authority in section 1031--should remain in force as to the overseas-capture scenario.
Bottom line: The Senate version of the NDAA is neutral regarding US citizens in the U.S., but certainly can be read to provide clearer statutory authority to encompass citizens abroad (so long, of course, as they fall into one of the categories specified in 1031). Note that the latter may not actually be enough to withstand a court challenge; if a court insists upon a "clear-statement" rule in order to construe the AUMF/NDAA to encompass citizens, this may not be enough to get over that hurdle as to foreign captures (and it certainly would not be enough as to domestic captures).