I don't think at this point you need to be worried about gender dysmorphia, that will become apparent as she gets older. However, you are not wrong to be taking her tomboy ness seriously and questioning how it may affect her in school.
In an ideal world everyone is accepted as who they are but it's not always like that in real life. My 9 year old has been a tomboy since she was about 3 and I will be honest, it has been very hard at times. I think she's starting to grow out of it and her interests are changing but having a little girl whose interests are so far from the current mainstream has been a challenge.
She's very clear about who she is but in her early years at school there was a clear division from both the children and parents as to what the girls did and what the boys did. She gravitated towards the boys but was excluded from the boys only parties / play dates / camp arrangements but didn't want to take part in the girls activities - she had no interest in ponies and dollies and making up dances.
As it happens we moved her to another school where they were far more accepting of her and she has thrived. I've gone out of my way to find activities for her to meet like minded girls and she now has a little gang of football playing girlfriends.
Step by step she's becoming more interested in "girl things" she likes craft, hammer beads, vlogging and Claire's accessories.
All along the way we have encouraged her to be who she is and to be confident of herself whilst being aware of social norms. We didn't let her cut her hair short, it's a short bob, she wears girls clothes but on the sports side so lots of sports shorts and trainers, hoodies and trackies so that she's comfortable but not so that she stands out too much.
I think / hope we have got the balance right and she's happy and confident without being labelled like too much of the odd one out.
It may be a short phase your daughter is going through but it may not be and you are absolutely right to question it and how to manage it in such a princess riddled society.
I bet she's fab, my DD is amazing and I'm so proud that she follows her heart rather than trying to fit in with something she's not comfortable with