Oh that explains it, I haven't done the after-alliance quests yet.
Which leaves us questioning who the last boss actually is. They could throw a curve ball shocker at us by it turning out to be Louisuix (with him turning out to have been the Sundered version of their creator), or just randomly make up a person on the spot to be the one we fight. Or maybe even having us fight their "caretaker." Middy 3.0 anybody? :p
I have thought about that before, because it would have made more sense for him to be the final guiding spirit instead of semi-resurrecting Minfilia (as a plot element if not physically) just to send her off yet again.
I think it's quite likely that they wanted to include him, but the optional nature of the Binding Coil storyline means that his soul is still potentially stranded there in Bahamut's thrall.
I would speculate that perhaps they got as far as putting him in that role, realising they couldn't use him that way, and hastily roping in Minfilia instead – thus the seemingly unnecessary business of pulling her back again after she'd had such a final send-off in Shadowbringers with F'lhaminn's sidequest.
The game treats everything as canon and done before (to an extent). Which is why Louisoix could appear. Krile and G'raha Tia are there, neither of whom met Louisuix. So the Coil stuff could easily be an extra line or two if you've done them, else you don't get that dialogue.
That is not how it works. If a sidequest changes the state that a character is in, then the MSQ alters dialogue to reflect the current state of affairs. If it cannot be covered with dialogue, it gets left out.
If a player has not done Binding Coil, there is a long-standing precedent that Alisaie's comments change to reflect our current completion state. If we left it unfinished, she says it is unfinished. If it's unfinished, then Louisoix's soul cannot be found in the Lifestream.
Iscah's right. Back before the Crystal Tower wasn't mandatory, the SHB MSQ reacted accordingly if you hadn't cleared it.
Same goes for EW's comments on Bozja or Dun Scaith when those NPCs show up, as well as the Omega quests and finishing Eureka (especially when Krile comments on Tsunjika's fate). The MSQ does acknowledge the content existing, but reacts to whether or not you've gone through it.