While I HAVE drawn Filly before, it was when she was still under Alexander's control; so she was still being forced to identify as a he and was simply 'crossdressing' to earn them Snails.
However; a truly out and transgender Filly would probably be something like this.
An illusion enchantment on a set of earrings to soften her features, and simple more 'peasant-like' clothes instead of primp and bawdy ones meant to show off and sell her body.
However; for her to transition in the Deadwardian era, she'd have to be outside of Alexander's sphere of influence, and for that to happen one of two things would have to occur:
Takara ( who belongs to my friend @angrymemesandicecreams ) would have to NOT fall through the time pool after beating the shit out of Alexander, and thus the misconception of her 'abandoning' Filly would never occur, and so they get to run away and live a happy life together.
OR
Alexander never finds Filly after she flees to the boiling isles in the first place. In this scenario, more than likely she takes refuge with the Fang Triplets, eventually marrying Blue Fang. They keep her safe and hidden, and since Alexander is looking for a man he never suspects the hooded 'witch woman' he sometimes sees around Bonesborough with one or all of the Fang brothers.
Of course; in both these scenarios, since it is inevitable that the Isles will be taken over by a dictator (It is, after all, a canon event) Alexander would take role of Emperor, and Filly (Very likely calling herself Filomena when paired with Blue Fang, though she still becomes Belia when with Takara) just probably dies of old age in the Deadwardian era surrounded by loved ones and actually genuinely happy.