I wouldn't be surprised if there are elements of culture clash. There are some parts of Heavensward that are quite difficult for me to interpret. Earlier, I alluded to Hraesvelgr being one of them: the game seems to think I will be appalled by things that I don't have a strong reaction to (e.g. Hraesvelgr saving Nidhogg), and that I will approve of things that I am genuinely appalled by (e.g. Hraesvelgr and Shiva). There are points in the paladin Heavensward storyline that I can only interpret as the localisation team attempting to apologise for how little sense the story makes.
The idea of service in the context of Thordan and the Knights Twelve seems like it could be another one. You do often find that Japanese media that apes a Western aesthetic nonetheless still has a Japanese soul; and vice versa, for Western media that attempts a Japanese aesthetic. In this case I don't know which cultural lens to apply. Ishgard is clearly making heavy use of Western aesthetic themes: the entire dragonslayer conceit is Western (Beowulf, Sigurd, St. George, even Sleeping Beauty), the Knights of the Round are of course Arthurian, and there's even a bit of Tolkien in the doomed relationship between the mortal and the immortal. (I mention these two specifically because Yoshida has mentioned being inspired by Arthuriana and Tolkien.) Yet as you say, underneath that something about the heart of the game beats Japanese.
I suppose I would like the story to be open to a plurality of interpretations, especially since Thordan himself is presented in so many ways: Thordan I, Thordan VII, and the primal King Thordan are all related, just as Saint Shiva, Ysayle, and the primal Shiva are similarly related. The plot of Heavensward revolves around the Thordans and the Shivas, and while the surface reading of the plot is that the Thordans are evil and the Shivas are good, I can't quite accept that myself. The heretic or draconic heroes of the story are all problematised. What is the ultimate difference between Thordan VII, and Ysayle, for example? They are both characters who commit terrible deeds for a good cause, and who clad themselves in primals. The game's position on Hraesvelgr is very odd indeed. And underneath it all lies this mysterious figure of Thordan I: the original sinner, but one whose character, motives, and goals remain obscure.
Anyway. I don't blame anyone for taking a purely negative interpretation of Thordan I or the Knights Twelve. That may well be the most consistent intepretation to take overall. Personally, though, I find so much of Heavensward's plot ambiguous. There are plenty of cases where I just don't know what it's trying to say, or where it seems to undermine what it's trying to say, or where it seems to be saying something earnestly but that thing is so prima facie absurd that I can't accept it as presented.