President Barack Obama signed the National Defense Authorization Act of 2013, better known as the NDAA, into law Thursday night, despite previously threatening to veto it over controversial provisions.

Obama’s decision to sign the NDAA into law despite his reservations about several key sections does not come as a major surprise to people who follow the White House, as he made a similar move with the 2012 version of the legislation.

But it is still a troubling choice, as Obama has repeatedly denounced sections of the 2013 version of the law that, among other things, re-codify the military’s year-old authority to arrest American citizens and detain them indefinitely without so much as charging them with a crime, hamper his ability to deal with inmates at the Guantanamo Bay prison camp, and render it essentially impossible for him to fulfill his 2008 campaign pledge to shut down the facility.

The chief purpose of the NDAA is to serve as a routine, annual spending bill, authorizing the U.S. government to direct funds to the military.

But over the past two years the Congress has saddled the bill with an increasing number of provisions unrelated to spending, some of which raise constitutional questions that Obama has publicly acknowledged.

So the question remains: Why did Obama sign the National Defense Authorization Act of 2013 into law if he has grave concerns about much of its content?

Let’s start with his formal discussion of the concerns he has with the bill, which came in the form of a so-called “signing statement,” a document the White House released in conjunction with the occasion of his signing of the bill on Thursday.

Signing statements came to prominence during the Ronald Reagan administration and gained popularity during George W. Bush’s two terms in the White House, and they are essentially executive branch decrees that lay out a president’s objections to a law, without requiring him to actually veto it outright.

Signing statements have been criticized for the past decade -- including by Obama in his 2008 campaign -- as being a convenient way for a president to sign a bill, but state objections to key parts of it, and to explain how they may be circumvented in practice.

In the case of the signing statement the president attached to the NDAA, he has done just that: First he presented a detailed critique of certain portions of the bill, and then he explained how he may direct the executive branch work around them.

His argument is that he is afforded certain authorities and responsibilities under the Constitution, and as such he may be forced – or choose not – to ignore certain parts of the NDAA if they encroach on those prerogatives and requirements.

“A number of provisions in the bill -- including sections 534(b)(6), 674, 675, 735, 737, 1033(b), 1068, and 1803 -- could intrude upon my constitutional authority to recommend such measures to the Congress as I ‘judge necessary and expedient,’” Obama wrote in the final paragraph of his signing statement. “My administration will interpret and implement these provisions in a manner that does not interfere with my constitutional authority.”

In other words, as Bush did repeatedly before him in regards to all manner of statutes (Bush issued about 1,200 signing statements, more than all previous presidents combined), Obama is laying the groundwork for a legal argument for not complying with specific sections of the law, though he does not explicitly state that he will take such steps.

This affords him the ability to sign the bill, but essentially propose caveats to how it will be interpreted and implemented.

Obama has also stated that despite any authority granted to him under the NDAA, as commander-in -chief of the armed forces and out of a certain respect for the Constitution, he will not authorize the military to indefinitely detain American citizens without charging them with a crime or allowing them access to a trial.

This is a shaky argument, however, because the NDAA of 2013 is now the official law of the land, and unless the authority to let the military engage in indefinite detention of American citizens is overruled by the courts or revoked via legislation passed by Congress and signed by a sitting president, there is nothing stopping future occupants of the White House from exercising that authority.

The stickier question is how he can come to terms with signing into law a piece of legislation that bars him from closing Guantanamo, or using federal funds to send its detainees overseas or even transport inmates from the facility to the United States in order to grant them a federal trial or other basic rights.

His signing statement goes even further in this regard, as the New York Times pointed out Thursday. Essentially, as many such documents have in the past, the statement serves as a guiding document for executive branch employees to follow when determining how to follow the new law.

“My administration will interpret these provisions as consistent with existing and future determinations by the agencies of the executive responsible for detainee transfers,” reads a relevant part of the signing statement. “And, in the event that these statutory restrictions operate in a manner that violates constitutional separation of powers principles, my administration will implement them in a manner that avoids the constitutional conflict.”

In other words, he is signaling that he may choose to act in a way that does not accord with the sections limiting his latitude in dealing with Guantanamo and its prisoners. But whether or not he will actually do so remains unclear, according to the Times.

“It was not clear, however, whether Mr. Obama intended to follow through, or whether he was just saber-rattling as a matter of principle. … Several officials said that it was not certain, even from inside the government, what Mr. Obama’s intentions were. While the signing statement fell short of a veto, they said its language appeared intended to preserve some flexibility for the president to make a decision later about whether to make a new push to close the Guantánamo prison amid competing policy priorities,” the Times reported.

Obama’s decision to sign the NDAA drew immediate criticism from human rights groups and other observers, who maintain that issuing a signing statement is not a viable alternative to vetoing a bill.

Shahid Buttar, the executive director of the Bill of Rights Defense Committee, was one such vocal critic, according to the Huffington Post, which reported that he had the following to say after the president signed the NDAA of 2013:

“It’s the second time that the president has promised to veto a piece of a very controversial national security legislation only to sign it. He has a habit of promising resistance to national security initiatives that he ultimately ends up supporting and enabling.”

Blogger Kevin Gosztola of The Dissenter went a step further, suggesting that Obama took the course he did as a matter of expediency and avoiding conflict:

“There were multiple actions the Obama administration could have taken to close Guantánamo that now become unlikely because Obama signed the NDAA … The president again chose the path of least resistance,” Gozstola wrote.

Obama also used his signing statement weigh in on the evolving issue of the religious rights of service members in the wake of the 2011 repeal of the "Don't Ask, Don't Tell" policy, and the way such rights are addressed in the NDAA of 2013.

The legislation that came across his desk includes a provision to ensure that the "freedom of conscience" of military chaplains and service members remains intact. In practice, the clause serves to ensure that members of the military - especially chaplains - are not required to engage in activities that are against their religious beliefs, including performing marriage ceremonies for homosexual couples, and that if they choose not to participate in such an activity, they will not be punished for that decision.

Obama held that the statute was unneeded in light of existing laws that deal with such issues:

"Section 533 is an unnecessary and ill-advised provision, as the military already appropriately protects the freedom of conscience of chaplains and service members," the President wrote in his signing statement. "The Secretary of Defense will ensure that the implementing regulations do not permit or condone discriminatory actions that compromise good order and discipline or otherwise violate military codes of conduct. My Administration remains fully committed to continuing the successful implementation of the repeal of Don't Ask, Don't Tell, and to protecting the rights of gay and lesbian service members; Section 533 will not alter that."

That portion of the signing statement has also already garnered criticism, including from Col. Ron Crews, a retired Army chaplain and executive director of the Chaplain Alliance for Religious Liberty, who offered the following comments, as reported by Daily Caller:

“Chaplains should be able to stand by their faith traditions and honor their commitment to God’s Word. That’s a freedom that Congress sought to protect, and the president is not at liberty to disregard the law,” Crews said.

In the end, it is difficult to ascertain exactly why Obama has now twice chosen to sign a National Defense Authorization Act that contains highly questionable provisions. But it is instructive to look at all the circumstances surrounding the decision when attempting to determine the thinking that led him to do so.