Except of course that they have all been Hurting Heroes since the death of Louisoix. Thancred's reaction to Emmanellain's words and actions was normal, not over the top: the kid hit him first, and Thancred's punch was not even really retaliatory. Besides, Thancred actually dealing with his feelings and expressing them not just through his actions but also his words to the WoL is a huge improvement for him. Unlike in 2.0, he isn't dealing with things by himself and letting them simmer to an explosive boil. I don't really agree with the part about Y'shtola barking orders either. If anything, she's openly expressing concern for all of her comrades, and especially for Thancred in advising him not to do something that could potentially be harmful to him. It's not like he couldn't have gone against her wishes if he truly wanted to, after all. To me, it seems like their bonds are strengthening. They may be more willing to make sacrifices, or at least more resigned to the need for those sacrifices, but as the gravity of the events they are going through is escalating, that seems rather normal. It doesn't mean that they will look for opportunities to throw themselves to the wolves, so to speak; it does mean that they've become more aware of and directly involved in happenings around them and are more actively protecting each other.
I'm not sure where you got that impression from? If anything, the Japanese version is more emotionally powerful thanks to both dedicated and extremely talented voice acting. Even the unvoiced dialogue tends to be much more powerful. Just in 3.3, for instance, rather than merely say Krile's name in the cutscene after the fight against Regula, Y'shtola outright asks if she is all right in the Japanese version. I can't actually recall any scene in the MSQ where this "manly resolve" you speak of is that prominent. If anything, you could hear Aymeric's voice breaking in the Japanese version as he told Hraesvelgr about the need to fight Nidhogg/Estinien. My general experience so far has been that where the Japanese version is exceptional in terms of both voice acting and written lines, the English version is either passable (when it is even accurate and not mistranslated) or mediocre (most notably the case with certain specific characters in 2.0). Even when a line is rendered accurately by an English voice actor, there is nowhere near the same emotion to it as in the Japanese version, where the voice acting reflects the talent required to perform in this industry, which is taken much more seriously there. With regards to Alphinaud, I imagine the main reason people dislike(d) him was because of his more arrogant-sounding English lines and the poor English voice acting behind him.