i usually try not to post the same things other moms have posted, but i thought in this case, the more people you knew could relate to you, the better.
the first time my mom took me shopping after i could talk i said, "mommy, no pink, no flower, no dress." all day long at school i waited anxiously to be able to come home & change into my dirty jeans & favorite snoopy sweatshirt. all of my friends were boys, i had matchbox cars, star wars figures & legos. i loved getting dirty & never, ever owned a doll. in fact, one time my maternal grandmother bought me a doll & i politely told her & my mom 'she would live at grandma's house.' i too shopped in the boys department exclusively. both my parents hated it, but they let me do it. i used to beat all the boys in my class at arm wrestling too ;-)
by the time i hit middle school my mom actually bribed me to get different clothes. it hurt my feelings terribly. i went through a brief phase with the popular kids & i did dress a little nicer then, but i found out they were so mean i went back to my roots so to speak. eventually i did go the punk rock route & that's when my parents really freaked. however, in 9th grade i decided one day to wear a skirt. it was of course awful looking as i had cut a dress apart & pinned it to leggings, but it was a skirt none the less. i agree with several of the other posts that cite puberty as a time for change in a girls attitude about her appearance.
i am now 35, a mom & a wife. i enjoy getting dressed up to go out (well, i did before i got too fat for my clothes). i wear make-up, get my hair cut at a salon, paint my toenails, etc. i'm still a tomboy at heart though. i love watching baseball, lifting weights & i'm quite attached to my hooded sweatshirts. the point is, it all evened out.
i also think current times tend to freak out about stuff we ignored years & years ago. no one ever thought i was gay, or trans gendered or anything. they just thought i was a tomboy, no big deal. just as you say your daughter has a crush on the high school musical boy, i had a huge one for luke skywalker ;-)
i know i can't quite understand what it's like to be the parent in this situation, but i wanted to at least offer my support from your daughter's point of view. i think your concern is genuine & as her mom you love her & just want what's best for her. my personal opinion is if you continue to show her love & support like you have been doing, she will be very appreciative & grateful for it as she gets older.
i would also say, if she decides she's no longer comfortable shopping in the boys department, don't make a big deal out of it. don't make her feel like you're so much happier with her because of the clothes she chooses. if you tell her you love her no matter what she wears, she'll be more apt to make her decisions from her heart, when she's ready.