What, transistions during the songs or in between songs? During the songs they'd just hit the clean channel, and in between Mikael would pull out his acoustic and play. There's plenty of amp modelling to make an electric sound like an acoustic, so they might use that. Bleak was played when I saw them headlining with Lacuna Coil for Deliverance - hell they even played Credence for that tour. Maybe they figured out an elegent way to handle it all last you talked to them.
The only time the flow was messed up was when Mikael started singing/playing the end to The Moor when he was supposed to decrescendo with the rest of the band into the quiet midsection
--Parv