While the story isn't shy of putting the horror out in the open with straight up Nausea Fuel, there's a fair bit of this.
Carol is described as being Younger than She Looks and very physically attractive to boot, looking about 20 at 14. The story explicitly touches on the downsides of this briefly, with a drunken Dirty Old Man grabbing her ass. While the guy gets put in his place after Bullying a Dragon in the form of T'Challa, as in real life, Carol is probably harassed, cat called and treated as a sex object who knows how many times a day by grown men, and probably has since she was 11 or 12, which has to be extremely traumatic. She's also got a Stay in the Kitchen dad, a mother who's implied to be of the Extreme Doormat variety and her only close family is her Cool Uncle, Jack O'Neill. Furthermore, she's implied, until Harry, to have only two close friends - Lex Luthor, who's something of Knight Templar Big Brother requiring her to be his Morality Chain and Jean-Paul Beaubier, who's Camp Gay and hiding his mutation - and a few less close friends in the form of her soccer team. A few throwaway lines have implied that just about every boy that's tried to befriend her has been looking to get in her pants, prior to Harry, and being regarded as a ballbreaker and a challenge. No wonder she's a little spiky and abrasive at first. And the more abrasive she got, as noted briefly, the more she's likely to turn off any of the few who genuinely do want to just be friends.
And when she really excels, at sports, beating all the boys, including the entire football team in arm wrestling matches, their fathers lean on the school board to get her tested for steroids. That must be incredibly humiliating - she's doing something that she loves and no one believes that she can be that good simply because she's a girl.
Jean-Paul also comes off as a Stepford Smiler - sure, he's extroverted, charming, funny and a Chivalrous Pervert that flirts with anything male, but his only friend is Carol (and then Harry), his twin sister is a mutant, psychologically disturbed and by all indications, only really responds to him. And since his father is the French Ambassador, that implies that his friendship with Carol is relatively recent. It also implies that it's on a countdown, since foreign postings only last so long. So, in a year or two, he'll be alone again.
Thankfully, as a Flash level speedster, this last is no longer as much of a problem.
Diana is an Empath and, by implication, has been one since infancy. Imagine growing up with a constant input of other people's feelings, good and bad, with no filter. After all, A Mind Is a Terrible Thing to Read. And, like the above, she's rather cut off from her peers. Not to mention, until very recently she lived in the Olympian court. Where the King and Queen are pretty much the poster children for Jerkass God. The Queen, Hera, in particular would like nothing more than to see her dead and Diana knows it all too well.
Asgard's revenge on Russia for the Red Son project is pretty awesome (especially in the older sense of the word), but how many innocent people will suffer and die for what Lukin is doing?
Why are there persistent, albeit mild (at first) shippy undertones to Harry and Carol's friendship? Because he's pretty much the first straight guy her age to treat her like an actual person for years - like, after she hit puberty - if not ever and she's the first girl his age to treat him like an actual person rather than a freak/saviour in pretty much ever. Even Hermione, after hearing his name, rattled off all the books she'd read about him in.
Why does Harry adjust so much less quickly during the temporary age up in Chapters 59/60 than his fellows, being described as barely scratching the surface of his powers? As one reviewer pointed out, he had so many more powers suddenly dropped on his head than the others did. Carol was just enhanced to Super Soldier levels of physical ability, Uhtred just became bigger, stronger and tougher, Jean-Paul became even faster and Diana's physical abilities were also jacked up. Harry, on the other hand, went from teenage Squishy Wizard to fully fledged Flying Brick in the blink of an eye, along with gaining vast Energy Manipulation abilities, seriously jacked up Super Senses, potentially vast Psychic Powers... the reviewer in question compared it to Clark Kent going from pre Smallville powers to full on sun dipped levels. He adjusted so much more slowly because he had so much more to adjust to.
Not only that, but Diana, Uhtred, and Jean-Paul are all used to their powers (Diana and Uhtred have had their powers since infancy, and for Jean-Paul it's been at least a few years), while Carol has always been a little above average anyway, and isn't getting anything new, per se, just being jacked up to the max of human potential. On the other hand, it's been only a few months since Harry's powers (other than magic) have begun to show, and less than six since The Reveal. He's still getting used to having all of those powers in the first place!
Carol's relatives descended from the same source, Peggy and Steve, all seem to have some unusual level of enhanced badassery. Except, seemingly, her mother. Jack O'Neill managed to become a Brigadier General entirely on merit at an unusually young age and has demonstrated a bit of super-strength while thoroughly pissed at General Ross for suggesting that they experiment on Carol. Sharon Carter managed to kick the ass of Baron Zemo's possibly enhanced protégé with relative ease, fighting on even footing despite his being considerably larger and the fight being in close quarters. And Carol had hints of it even before the incident with the Genius Loci. This suggests that the abilities aren't entirely dormant and only require a relatively small kick in the genetic pants to activate.
With all of that in mind, it's very likely that instead of the upgrades skipping her, Carol's mother has the same potential abilities, and chooses to be an Extreme Doormat because she's terrified of what she's capable of.
Going by her appearance in chapter 6 of Ghosts of the Past, she's no doormat of any kind, and is later confirmed to have Refused the Call.
It's stated that at some point before the story, Gravemoss dueled Doctor Strange and survived. Is it because of Gravemoss's combat skill, or because Strange let him survive, so that Gravemoss could raise Chthon and thus play his part in his defeat?
A small one, but in Chaos Reigns, Harry Dresden mentions that Murphy has big dog issues. Perhaps due to having fought werewolves in Fool Moon?
Sure seems like a Contrived Coincidence that a young, Omega-class mutant just happens to be skiing on a mountain with a genius loci, and that the Avengers, Harry, and his friends are all there at the same time that he's most vulnerable and HYDRA are most likely to make a grab for him. Knowing Strange's MO, it wouldn't be at all surprising if he'd arranged that, too, somehow.
Why did Strange get so spectacularly worked up about saving Maddie, to the point of being Driven to Madness? Because way back in the day, after he arrived too late to change the outcome of the Battle of Camlann, which led to the deaths of almost everyone he knew, his mentor nearly going mad with grief, and his home and everything it had stood for crumbling around him, he made a vow to never, ever be too late again. This, from a man who never, ever lies, whose word being questioned is a personal Berserk Button, and a magical practitioner of almost unrivalled power in a world where an oath made on one's magic has very real consequences. Not only was he guilty about failing, but his vow would have kicked in. The Fridge Horror, of course, kicks in when one wonders just what it would have done to him, and what would have happened to the universe without him...
The Reveal in Ghosts of the Past that Gambit was artificially aged and "born" at about seven explains why he's so flirtatious-given that Carol estimates his age at about nineteen or twenty, he's really a Hormone-Addled Teenager!
A minor one that gave this troper a good chuckle, Harry is from the Grey Family and Draco is distantly related to the Frost family and now their rivalry makes sense. Frost's and Grey's have never gotten along.
The occasional descriptions of the American magical world as more liberal and open to Muggles than its British equivalent seems pretty much the opposite of the canon MACUSA's attitude (cf Fantastic Beasts and Where to Find Them). But then the Fridge Brilliance kicks in-this is a magical community heavily influenced, if not outright run by, Fury and SHIELD. Of course it's more open to Muggles.
There sure are a lot of Adaptational Badasses in this story. Sirius going from being a skilled duelist in canon to having the Red Baron of "The Marauder" and being picked for the Shadow Initiative, the Winter Soldier becoming The Dreaded for just about everyone, Sean Cassidy being able to do far more with his Make Me Wanna Shout powers and having Boxing Lessons for Superman, etc. Makes a lot more sense when you consider that Strange is setting up Earth to go against Thanos, and all of the upheaval caused by Chthon and the resultant aftereffects, and presumably therefore wants every advantage he can get.