Lug nuts being unevenly torqued is DEFINITELY a source of rotor warpage.
I have been pattern torquing lug nuts since the seventies on anything I've touched with disc brakes. I'm also careful at the tire stores and such to see that I tighten the lugs myself (who says I'm anally retentive?)
So, I'm quite certain that this is not the source of warpage on any of my cars.
Have a great day,