Obviously, I disagree otherwise I wouldn't have presented her as an example.
Well, it's an example of you citing something as a "Mary Sue" that doesn't actually fit that definition. The defining characteristic of a Mary Sue is that she has all the usual characteristics one expects from a hero, but carried to a hilariously excessive degree
purely for the satisfaction of the author.
Basically, the character version of the Scimitar: it's got 52 disruptors and 26 torpedo launchers, double layer shields, a fighter bay, a flesh-melting wave motion gun capable of slagging entire planets, AND it can fire while cloaked. A villain being hilariously overpowered just sets your protagonist up for an underdog victory, but when the HERO is hilariously overpowered, the writer is either screwing around with wish fulfillment, or he's going for satire.
As far as I'm concerned Rey and Burnham have been designed to possess whatever traits required to satisfy both in story presence and wishful expectations of society in general.
That's entirely possible, yes. But that's not what a "Mary Sue" is.
A character that acts as an avatar for the wishful expectations of
society in general is an "archetype." Superman, for example, is an archetype: he's a strong, virtuous hero who always does what is right even at great personal expense. Superman is hilariously and almost disastrously overpowered, and his writers have at various times just pulled new powers out of their ass just because superman needed a way out of whatever hole they had written themselves into. But superman is not a Gary Stu, because he isn't an avatar for THE AUTHOR. He's an avatar for the kind of hero the author (and by extension, society) idealizes as the ideal protector, which is one of the reasons why more modern treatments of superman lore have almost messianic overtones.
Put this another way a writer who creates a story about finding The Perfect Girlfriend isn't creating a Mary Sue character. The writer whose protagonist IS The Perfect Girlfriend -- especially if this is done unironically -- most likely is.
Is it bad to have these characters guaranteed a rite of passage whereby they upstage everyone else? I suppose not, but it doesn't go unnoticed.
Indeed. But it also isn't a characteristic of Mary Sues.