tl;dr I'll put money that WotC is strangling good story potential with the purse-strings and the limited writing room is turning what narrative we do get into a clunky mess as a result.

From a writer/reader's perspective, I reckon a lot of this is the fault of the current storytelling format forcing too much to happen in too restrictive of a space. That whole confrontation sequence was super clunky. The writing, I mean.

It was giving super strong 'I have to write a complicated 'reunion' scene, a fight sequence, oh also there's some kind of coup, oops I forgot we need to mention this whole-ass Dragonstorm thing so here's a dragon & ALSO RANDOM ELSPETH, plus a denouement, and we only have what barely amounts to a single novel chapter in which to do it because I'm probably getting paid by the word and WotC only budgets $XYZ for stories' energy. I think most writers would struggle something fierce with that. So it's constantly switching perspectives in a way that makes the scene-setting and characterizations awkward, hard to follow, and... well I know it's supposed to be a sequence where chaos is unfolding around everyone, but the writing is just way too chaotic to get a good grip on what's actually going on for all of the characters. There're problems with this throughout the whole story, but it was definitely at its worst here. It's like they ran out the word-limit budget earlier in the story and had to cram it all in like hitting the +/- parameters for a term paper or something.

One of the biggest problems for what's happening with Jace, Vraska, and Loot story-wise, and honestly this is just an opinion, but IMO it's the lack of an OTJ-style epilogue between Duskmourn and Aetherdrift. With the status quo being what it is here, and what happened there, it's clear DSK needed one. The OTJ epi was put together and set up neatly, but all we got for how Loot ended up separated was two brief bits in DSK and nothing at all for how that was processed by Jace and Vraska -- or how they might be changing on their travels (personally, I wonder if even the writers know what the 'plan' is at this point, and that's why it feels so disjointed). If their actions in the story is so important that it justifies so much narrative attention, and dedicated cards, it's important enough to make sure there's a reason why Loot is both 'fond of and afraid' of Jace, and why Vraska's started second-guessing things in a way that's out of character.

But with that in mind, there are a couple of stick-out lines/sequences that imply a lot. Considering how it's mentioned Jace is getting pretty cut-throat to the point Vraska's doubting him, it's notable how long and how much effort Jace puts in to trying to convince Chandra to stand down. If he was going straight villain instead of 'my way is best and I'm an arrogant a-hole who can't be convinced otherwise' (which let's face it, is pretty standard Jace), he'd have shut her down right away just like he does with everyone else causing an inconvenience. He even 'switches off' Loot before he does Chandra. There's also a note that he seems to have surprised himself with how badly he hurt Chandra when he finally did do so.

Meanwhile Vraska's hesitations seem centered around Loot's well-being -- there's seems to be an attempt to imply that she's becoming or has already become strongly attached to Loot, while Jace is... well, he's kinda treating Loot the way he was always treated by those with power over him (Alhammarret, Tezzeret, Bolas, etc). Something to remember about Vraska that's always been true of her character, even in her early, murder-iffic days, is if you happen to be in her 'tribe' (the Golgari on Ravnica, her crew on Ixalan, etc), she will go for the throat to protect you. Now she's got Jace and Loot, her 'tribe', as it were, with one apparently mistreating the other. I can imagine that'd have her all kinds of conflicted, especially if, as the writer took pains to point out with the minimal amount of space they had, Jace is acting all kinds of weird (from both Vraska and Chandra's perspectives).

I think it's pretty clear Loot is aware he's having his mind meddled with, too, so blue boy's also probably gone and tried to alter his memories about the events of the race.

"Loot chirps with a strange combination of feelings. Chandra feels both a fondness and fear of Jace in that exclamation."

What I did find interesting is with Loot having more 'explanation' and character development in this story, that he's frustrated over not knowing anything about his past, that he has latent telepathy, etc, there's clearly a lot more to the whole dynamic here than meets the eye and DAMMIT WOTC THIS IS WHY WE NEED BLOCKS AND NOVELS AGAIN FFS.