As John himself says, he can now walk into any retailer and take a SS off the wall and it will feel, play and sound the same as his own personal models.
That doesn't mean that he doesn't have some SS's, particularly prior to release that were 'prototypes' - different Radius, different frets etc that were sent out to test and the feedback from John used to refine the specs. No doubt John can get 'special' versions made just for him - whether its a Maple fretboard, special/limited colour, maybe a bound fretboard etc etc that may show up on stage but may not make it to a retail version.
You never know if he is playing a 'retail' version, a 'prototype' for maybe some new version (like the Maple fretboard model or new colour choice) or a special, personal edition gifted to him from PRS.
Mark Holcomb and Zach Myers both use their 'SE's' a lot. I believe Holcomb will replace the tuners for locking tuners but both use their SE's as well as 'core/PS' versions they have 'bought' from or been 'gifted' by PRS. Taking 1 photo/song from a show as definitive proof they don't 'use' the same guitars we can buy doesn't really tell the truth...