The answer is plainly yes, but I'll add an explanation regardless:
The concepts of 'cis' and 'trans' don't exist in Arsur because no one is assigned a gender at birth. However, from our own perspective, we can obviously still label characters as trans or cis based on our standards. For example, if you have a character that would have been assigned male at birth by our standards but considers themselves otherwise, they're obviously a trans character to us, even if the concept doesn't apply in universe because they were never misgendered and socially pressured to be male.
Similarly, body transformations are also used in-universe for a variety of reasons, including to better match someone's identity even if gender assignment isn't a concern. You obviously don't have to physically transition to be trans, but the option is definitely there!
It's not something that will be explored in the game though, it's not really a focus of character development for MC: they are comfortable with their identity at this point in their life. Of course you are free to headcanon that your MC used a body transformation themselves when they were younger to fill in the gaps!
That's also why I didn't make the player specify their Crown's gender and sex in-game, only their pronouns - whatever you imagine for your Crown's gender and their experience is fully up to you and is equally canon to anything else.