What shows up on the boarding pass can indeed be distinct -- in one or more ways -- from the passenger info entered into a PNR and transmitted to some government(s).

For example, a person whose traveling from the US abroad on US passport has a given name of Nicholas Mir with a family name of Svensson in the passport. He could have a ticket purchased as Svensson Nick (i.e. reverse order to what is common and with an abbreviated form of Nicholas). The boarding pass printing out with the name NICK/SVENSSON, and the (In)Secure Flight info transmitted having the name first name as Nicholas and the last name as Svensson. There are lots of permutations of such that get transmitted and processed.