So, if it's an "always been a girl/guy AU" not a "hey, how did these get here?/where the heck are my boobs?!" scenario, how do you handle the character's altered gender expression? Of course, since they're the same people, they'd keep the same interests, but having stereotypically masculine or feminine hobbies doesn't necessarily translate into one's overall butch or femme-ness (I've known more than one conventionally manly guy who was interested in both cooking and textile crafts.)
So, if you're writing an AU version of a very manly Even The Guys Want Him action hero, do you make her a badass hot butch girl or badass, glamorous and feminine in a hard-edged sort of way (sort of a grown-up version of the Tall, Dark and Bishoujo aesthetic, although she might not fit the physical stereotype)?
An odd thing if you go with the butch option is that a really manly girl has a different relationship to societal gender stereotypes than a really manly guy does, which may be of interest to queer theorists and femslashers out there.