Hydaelyn and Zodiark did clash, though it simply wasn't shown. The Elpis finale is little more than a stylistic and false depiction of the events that took place in a desperate attempt to deflect attention away from Venat being the one to set all the tragic events in the setting into motion.
My guess is that they didn't show a battle between Hydaelyn and Zodiark because doing so would clearly paint her as the aggressor and showing the actual Sundering taking place would further showcase just how awful a process it actually was.
Which in itself is a large part of the problem. The game had no issue showing Zenos grabbing Yotsuyu by the hair, or having Yotsuyu manipulate a villager into killing another. Or showing the gruesome effects of Black Rose. Or having Valens gleefully torment his underlings.
The game chickens out, however, whenever it comes to showing the supposed 'good guys' getting their hands dirty. It's a very childish approach and cheapens the better elements of the story elsewhere.
As much as I like Hien, for example, the whining about Garlemald's 'war crimes' seems pointless when he flooded Doma Castle and sent whoever was inside of it to a watery grave. Let's be honest - if the Garleans had condemned a bunch of Domans to a gruesome death through drowning and being crushed by debris, we'd never hear the end of it.
For me, it's not so much the acts themselves that bother me so much as the hypocrisy.
I frequently ask myself why the game insists on inserting lengthy lectures about heavy topics only to look the other way every single time one of 'good guys' does something worthy of contempt.
Personally it's why I don't consider the Scions or the player character to be 'heroes'. They're nothing of the sort and simply drift from place to place in order to force everybody else to adhere to their specific set of ordeals whilst also calling out anyone else who dares to do the same thing.
More than anything, the game's inability to own up to the questionable deeds of the protagonists is bitterly disappointing for me given that I usually find myself deliberately picking out the darker and more nuanced options in the various games that I play.