My experience (version 2.1, downgraded from 3.0 because of a bug).

1. I freed Scyorielaphas.

2. Allied with Rauatai.

3. Got involved in the naval battle.

4. Monster appeared (didn't occurred to me it could be the guardian) and Scyorielaphas fought it off.

5. Arrived at an empty Ukaizo harbor - which was a bit anti-climactic as I expected a fight as difficult as the one with Thaos in PoE 1.

Captain Furrante arrived after I shut off the storm machine, but that fight was too easy on normal difficulty with a level 20 party.

 

 

Ok, so there's at least an actual scene in the game where the Guardian appears and Scyorielaphas fights it off? It's not just "guardian goes poof" ?

 

 

I just finished a run where I freed that Scyrioelphas and I mean... it's an interstitial card in the scripted encounter, but if you're quickly skimming or just mashing the "1. Continue" button you might miss it.

I have to agree that I'd prefer the final boss fight not to be skippable "by accident", and I'm kinda glad the bug existed when I first beat the game. From what I see in videos on youtube or twitch, too, the reaction to Scyrioelaphas fighting the Guardian in your stead is less of an "awesome, I found a way to get around fighting the final boss" and more of a confused and slightly disappointed "wait, this game doesn't even have a final boss?". I think the reason for this is that you make the decision to free Scyrioelaphas many hours before the game ends, it's a "good guy" decision so most players will choose it, and it's not immediately connected to the idea of getting around the final boss battle. Player aren't aware that not having a final boss battle is a  direct result of their choice, and it feels anticlimactic. In my opinion, a better way to have freeing Scyrioelaphas matter would be to have the Guardian start the final battle wounded in that scenario.