Have it be that dysphoria/gender questioning prevents the Spark from manifesting. Per RJ, there's no guarantee a channeler born with the spark will have the spark in the next birth. They can be learners. Or vice versa. And he's said that it's very very rare for a learner to stumble onto the Power on their own. So clearly the spark/learner distinction isn't tied to the soul.

Have it be that someone who is trans and has dysphoria usually can learn to use the half of the Power appropriate to their gender expression, but they don't figure it out, usually, because per societal expectation, you only channel the half tied to your birth sex. They rarely explore this, so it's rarely seen, but Moiraine and Siuan, who delved into False Dragon lore deeply because of what they knew, discover that it HAS happened, if very rarely, so they keep an eye out for someone who is female, too, and don't write off the possibility.

The rest of the world, however, assumes it'll be a dude.

I have other alternatives, but I think I'm just going to make a post exploring the various ways RJ's world is very easily molded to a non-gender essentialist view.