The classism theme and Alm's status as secret royalty makes much more sense when you consider it from the lens of noblesse oblige. I think this is part of the reason why Fernand and Berkut were added and why Slayde became much more prominent. The idea behind noblesse oblige is that the nobility have social responsiblities that they must fulfill for the commonfolk in exchange for their wealth and status. Clive, Fernand, Berkut, and Slayde all represent different aspects of the nobility when viewed from this lens. Clive is a positive example of the nobility and strongly believes in noblesse oblige; he believes that a class system is necessary, but he still treats the commonfolk as actual people and is willing to acknowledge their abilities. Even when he suggests not saving Delthea, it's because he sees it as a regrettable sacrifice to save everyone else, instead of thinking she simply doesn't matter at all due to her blood. Fernand serves as a foil to Clive in that he's somebody that lost faith in those ideals, as from his perspective, they led to the death of his family. Berkut believes in a somewhat corrupted, Darwinist form of Clive's philosophy; his motivation is to prove he's worthy of his position, which suggests this is something he expects from all nobles, and his low opinion of commoners is based on the belief that they are inherently not strong enough to ever earn such positions. And Slayde represents the worst examples of the aristocracy, particularly the extreme sense of entitlement and the callousness towards everyone else; he doesn't even think about whether he's worthy of his position like Berkut does, and just takes his status for granted.
In regards to how Alm, his status as secret royalty doesn't undermine the main point regarding class that the game was taking, because it was never that one's social status doesn't matter. Rather, it's the idea that one's social status doesn't necessarily relate to their quality of character or their ability, and that people with high status are only worthy of it if they accept their responsibilities towards the happiness and safety of their subjects. Furthermore, Alm spent his life living like a commoner, among commoners. The scene in Act V where he talks about showing Clive how to use a plow is meant to highlight that even after the truth of his birth is revealed, he still has the same moral compass and the same empathy for people he previously had. Also, Forsyth's, Gray's, Tobin's, and Jesse's endings are all examples of peasants rising to the nobility, Jesse even founding his own nation, all entirely due to their merits.
In regards to Ceclia's alleged idiocy, I found this was actually handled surprisingly well for the most part. Contrary to popular belief, Celica DOESN'T immediately buy Jedah's claims, and in fact questions what makes her so special that she could help with Duma's madness. The reason she ultimately caves has to do with her own lack of faith in mankind's ability to fend for themselves, the same reason she set out on her journey in the first place. It's also pretty obvious that Celica doesn't want to do it either but from her perspective, there are two options: 1. Duma degenerates, Mila doesn't come back, and the world is fucked, or 2. Sacrifice her soul on the chance that it might help Duma not go crazy, which would ultimately have a higher net worth. Celica not telling the others about it is very in-character too, she doesn't even Mae much about Alm, and both Kliff and Mae remark how she tends to keep things to herself and not burden other people. The main reason why it comes off so much worse is because Jedah's character design is way too...extreme to put it lightly. Even keeping the blue tinge is fine, since that seems to be a thing among the Duma Faithful, but looking normal would go a long way to make Act IV easier to swallow.
(I also find it ironic that there are a couple of people who hate Alm but then praise Robin in the same breath. The cognitive dissonance is amazing).