I don't understand why his reaction to Envy would be only vague alarm though. If Envy's civility was shocking, then why wasn't Alphonse shocked? It's especially glaring since reactions in FMA tend to be grossly overexaggerated for the sake of humor, like Ed's screaming reactions to being called short. The range of emotion I've seen out of Alphonse so far has been confused, vaguely upset, or as you said yourself, vaguely alarmed. Even if he's being cautious, he shouldn't be flat and one-dimensional.