I like to think that Madeline experiences gender the same way I do, which is to say, we're… women? We guess? Like we don't feel a particularly strong connection to being women—or the concept of gender at all, really—but we don't feel particularly dysphoric about it, either. (Unless it's in the context of a man being attracted to us, no thank you.)
The closest label I've found for myself is demiwoman, which I only felt compelled to seek out because neat categorization pleases my brain, but… You know how some people say "my gender is lesbian"? And how the only time they feel like women is when they're loving other women? That feels most like us.
Either way, I definitely don't think Madeline would be applying that level of introspection to her own identity before we reunite. She'd just call herself a lesbian and be done with it. I don't see that changing much after we get together, either, she has lots of other areas of study she'd rather spend her time thinking about than her identity.