Well, is Arthur Maxson fighting for the betterment of the Wasteland and Boston? Or is he just a raiding party? Given the overall altruism attributed to the Lyons faction, I'd stick with him as a necessary evil. Even if it isn't him, I trust the CWBoS to hold to the Lyons Doctrine; if I find them wanting and clearly just a pillaging force a la West Coast BoS... then, no.
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Given this is their third, this one will be bigger than the previous two. To be honest, the armament they seem to have and the dedication makes it sound like a crusade; and humans don't **** around with crusades.
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I think 101 will be mentioned and establish a "better" canon ending. There's no way the CWBoS could recover and mount three expeditions if the Citadel was destroyed.