Generally people do not choose whether they are gay or not, they are born that way. It doesn't matter and is NOT a big deal. Just accept her for who she is and let her express herself. It could just be an exploratory phase that she is going through and she may change her mind later. Don't make a big deal out of it.
My sister did this, wore the jeans all the time as a kid and liked her hair short. Turns out, she's gay, (although not trannsexual. She doesn't believe she is a boy or anything like that, and in fact had a baby and was a great mother including breastfeeding and the works. So she doesn't have gender-confusion issues, she is just someone who resonates to women as romantic partners instead of to men.) I don't know if the liking the short hair and jeans when she was a kid was a signal of what was to come in her life, or if it was just coincidence.
I will say, if that is why your goddaughter is doing it, just be her friend. So what if she wears boy's clothes and walks with a "slight boyish sway!" (why the exclamation point? Does it alarm you that much?) Let it go, who she loves romantically when she grows up is not the biggest worry in the world. Better she be a lesbian and have a great relationship than a confused 17-year-old who is going to bed with any man that will tell her a good line. Be there, so she won't be a confused 17-year-old with nobody to talk to that has her back.
There are a couple reasons why girls do this. Some girls live in situations where it's better to be a boy - in their lives, being a girl causes them to be abused or less valued. This doesn't sound like it's the case in this child's life
The other reason is they believe they are boys. There are theories that their brains are actually male brains and only their genitals are female, and theories that it's still a choice.
Chaz Bono recently came out with his transition, it might be worth listening to his stories.
http://www.cbsnews.com/8301-31749_162-20062573-10391698.html