I mean, Naoto still wears male clothing and identifies as a male to the majority of the characters in the game. Like I said, it's left somewhat ambiguous. Her doing "girly" things is behind player choice as well, besides the somewhat cringy "I'm glad you were born a girl" line that's silly and creepy that you have to do to get on her romance path. Overall, I think you could make a case either way, which you could either blame on the writers not making it clear enough which way they were going or purposefully making it ambiguous to let people decide what they would prefer Naoto's story arc to be.
This discussion is a bit off-topic, though I'd love to discuss it more (most conversations about Naoto, probably due to the nature of the Persona fanbase, end up pretty one sided). Perhaps a thread elsewhere would be better.