I sent out a group e-mail to the subscribers of the Pop-Analysis interest group for the Society of Music Theory. All replies have confirmed that Method 3 (i, bIII, iv, bVI, bVII, etc.) has become the standard technique among theorists and pop musicians. To quote a pre-eminent theorist in the field of pop/rock analysis:
“[Method 3] has been used in rock guitar method books and magazines going back to the 1970s, as I recall, and I suspect in jazz improv and theory books going back even further. I’ve always used it as my default with no sense that the major key is anything more than the easiest neutral place for comparison and orientation.”–John Covach, Director; Institute for Popular Music, University of Rochester
No one seems to know of any specific arguments for Method 3 in print, at least in terms of addressing its use over the traditional method (Method 2). But all seem to agree that it has become the de facto standard.