It's possible, Alphinaud would want to focus on more diplomatic issues, rebuild the Crystal Braves, and lead the Rising Stones as I could imagine the Dragonsong war was taxing on him.
I'm inclined to assume about Thancred that we could find out that Minfillia's fusion with Hydaelyn is actually a tricked/forced abduction and the Ascians knew. Alisaie could easy spill the beans and he'd be the first to know... and he already feels pretty bitter about being unable to get Minfillia back. I get the feeling as WoL we aren't getting the full story and Ascians would rather play us as pawns than tell us straight. There is a faint hint with the W'soD that at some point Elidibus might of convinced them they're following a falsehood...
Or, they could be converted into Zodiark's thralls that were taken when Louisoix ported them away from the planet (The opening ARR cutscene) before Bahamut would finish them off. Even as powerful as Louisoix was, the Binding Coil story explains how he was being controlled by Bahamut when you see him in the SCoB cutscenes. We did see a CS of the W'soD attacking an Ascian in 3.1 in a place similar to when we talk to our crystal only to fade to white moments later.
EDIT: Come to think of it, this thrall thing, my jaunt through all of coil recently opened up some possibilities... Elidibus seems to be the most approachable character among his associates, oddly clad in white, while still having a dark secret he's keeping but right now he's on good terms with Urianger and assuming he's Unkawhatshisname (Kid-lidibus) master. I'll bet he has a much grander scheme and has been using the other Ascians... who also might just be merely thralls of Zodiark as a means to an end. Where as Lahabrea and co. want Zodiark to revive, where Elidibus seeks to reunite Zodiark with Hydaelyn... which might explain how Urianger seems to be "going along" with this idea so to speak.