I saw Opeth in London on Saturday night (19th Novmber) at Wembley Arena and noticed a few things above previously mentioned:
-Marshall full stack (no head) on stage and not mic'd up
-No visible rigs - couldn't see heads being used or Axe FX in a rack anywhere
-Amazing acoustic sound when playing the clean/acoustic parts.
I would conclude that they had used a tone match on their Axe FX of an acoustic as it sounded very convincing. Blindfolded, I would have guessed that they switched to a real acoustic for those parts. Not sure if they are using Piezo pickups in their electrics in addition (or in lieu of) tonematch but they both have PRS customs and didn't seem to be using their SE signature models.
As always, a great show and fabulous tone from Opeth