They’re all listed as variant covers (e.g. you can see the regular Thor #3 cover, here).
The only people who would see these covers are people who have specifically gone out looking for Carol Danvers 50th Anniversary variants, which will likely have much smaller print runs and may have a premium price.
Perhaps it’s worth pointing out that it’s the 50th Anniversary of Carol Danvers, but not Ms. Marvel. Carol was a supporting character for about a year or so before dying (!) in an explosion, not showing up again for about 8 years until the Ms. Marvel comic debuted in 1977.
Also worth noting that she was treated horribly as a character by substandard writers well into the 80’s (Avengers #200 is a low point for Marvel.)
She was a side character/guest star to the X-Men and a few other teams until finally rejoining the Avengers in 1998, and then Marvel really started using her right in the 2000’s with her own book again, etc. She’s only been growing in popularity since.
That’s a good question. We usually only do cover art changes like these for special occasions, so I’m honestly not sure what it would take to get alternate cover art into the game on the regular. (I like the idea though of it being a permanent game feature though!)
It’s happened before. A number of characters had cover art that was replaced when the special themed cover for an event proved more popular. Mostly “Women of Marvel” varients.
Squirrel Girl, X-23 and I believe Thoress are examples. We’ve also had covers just permanently change for no obvious reason, like 2* Daken and 2* Ares.
She hasn’t worked in recent years in the comics, because no one who is writing her has done anything interesting with her as a character. They keep giving her new roles in the MU (Captain Marvel, then GotG, the Ultimates, then leader of Alpha Flight), but did nothing to enhance who she is at the core. Chris Claremont and Brain Reed were the closest to making her into someone to care about. But this is where the movie has every advantage. It’s a fresh start to do something interesting with the character that makes her standout in that world. And I hope they can do it, because Carol is a character I want to like, but has never really worked.
That’s like saying you should root against Captain America if he was fighting a bank robber. Admittedly, there’s a lot of crap, as there is with any long running superhero, but the best Superman stories are ones that shine a light on how he’s someone who cares about everyone and wants to inspire people to be better. Read All-Star Superman. It’s self contained and highlights all the best aspect about the character.