I think that both the original article and your alternative version are violations of FumbleFingers' Perfect TruismFumbleFingers' Perfect Truism, namely ”Don’t use Past Perfect unless you really have to.”
The text makes perfect sense if you eliminate all of the past perfects:
This is not the first time that the Bollywood actor has been detained at a US airport. In 2012, Shah Rukh Khan was detained at New York airport for over two hours by immigration officials. The US customs and border protection authorities expressed "profound" apologies for the Shah Rukh Khan's detention then.