I think the origin that Orci & Kurtzman came up with was brilliant (and those that know me know that I don't use Orci, Kurtzman and brilliant in the same sentence very often).
According to Karl Urban, he adlibbed the "Bones" line at his audition, and everyone laughed so hard they added it to the script.
As with all the best nicknames that stick, they often have more than one meaning. Certainly the nicknames I had as a kid (and young adult) had several shades of meaning each, depending on who was saying, or overhearing, them.
BTW, Alan Dean Foster hated the "nothing left but my bones" reference and changed the line to "skeleton" in the movie's novelization.
I think it was Abrams who said it in the movie's commentary that Urban came up with that while filming the scene, it was not scripted.
In the audition
. According to Urban at a Sydney convention a few weeks after the film's release. During actual filming, the script was "locked" due to a writers' strike.