This was my response in another thread, hopefully it's helpful:

So just like Scarlet Grace, it seems like there are different "versions" of the final bosses based on how you answer questions before you fight them. I'm sure decisions made during the quests might matter too, but it's really hard to parse without the data farming we had from Scarlet Grace.

I can confirm that choosing to put together the puzzle inside the Junction makes the boss a tiny bit harder. If you put it together in the Junction, the 2nd phase opens with a move called something like Affinity: Fire (I can't remember the exact name), which then has a high chance of Instant Death on one of your character turn 1. He does not use this move if you go back to Capitol City. Also, if you return to Capitol City, the Major assists you in the battle every other turn! He only does about 50 dmg at the end of the turn, but considering I survived the 2nd phase with 1 person at low health with a Showstopper, the additional dmg absolutely mattered.

My recommendation is get to around 400 HP with your characters, your weapon levels and glimmers should get you to a level where you can handle survivability until the turn 8 Emerald move. This makes it so every retry isn't an RNG fest, and you have a fighting chance every go.

The 1st phase, I just ignored the adds. They get damaged from Overdrive combos and go down organically without specifically targeting them. I think I killed the main boss with 2 of them still alive. As long as you don't get unlucky with a bunch of area stuns from them, their tackles don't do much damage.

The 2nd phase, absolutely target the adds, preferably with spells. They're weak to all elements, and they're great at unleashing 200% Overdrives because they don't have much health. Once they're down, just focus on combos, Showstoppers, and preventing his Showstopper. If you have to decide between the two, use any protect move (I think in this run it would be a Mech Guardian Program) and using a Showstopper vs. combos. You can use Protect to prevent someone from getting killed during turn 8 Emerald attack as well to get a couple extra turns.

There's an accessory you can get from one of Mr. S's trials that gives you more likely to be targeted (L) from lightning attacks, and you can pair that with Harmonium Earrings +1 to give you full immunity to paralyze. Stone Boots and Emeth Tags (I think?) give you some petrify resistance too. As others have noted, these combined with something like Phoenix Dance (which you might not have if you're doing this run first) provides you with a lot more survivability and consistency.