I think everyone else is giving great advice, and I just wanted to add to the voices lauding you for being so proactive on your child's behalf.

I have a rather unique experience in the gender world, because I didn't start puberty (specifically, menstruation) until I was 18. Before then, my mom forced me to go to gynecologists to figure out what was wrong-- basically, among lots of other mental health issues, I was anorexic and exercised too much, which caused primary amenorrhea. Going to the gynecologist without an explanation of what they would do (or touch) was traumatizing; being forced to take a pill that would force me to bleed every few months was also traumatizing. Sure, my bone density may have been protected, but at a steep cost to my mental health.

What I didn't realize until much later in life is how utterly defining a delayed puberty was for me. I spent all of my youth effectively as a non-sexual human-- literally, incapable of reproduction and with a (dysfunctional?) sexual system. Even though I often felt left out of women's discussions at the time-- even though I was often ridiculed by "blossoming" girls at the time-- I now cherish that phase of my life. It took me a long time and lots of therapy to realize that my "genderlessness" was basically established during those tumultuous teenage years.

All I'm trying to say is... yeah, it could be a phase. But the next few years of your child's life are also going to shape who she is for the rest of her life. That "tomboyishness" isn't going anywhere. That questioning spirit isn't going to die down. Her clothing and hair and outward appearance are going to change, but there's a kernel of truth inside that is starting to grow, and it will keep growing. Please nurture it, keep the doors open, ask questions, be curious, and support her. Express caution when necessary, but always cushion it in discussion and openness. Only she knows who she is-- and whenever you're not sure, just ask.