Since day 1 of Ten Desires drop they've been like that, though to be fair ZUN's interpretation of Prince Shotoku borders on that trans fuckery a bit. Not outright "trans women r women" but he's basically just implied that Prince Shotoku in Touhou canon was actually a woman the entire time, despite everyone calling her a prince, and the whole process of becoming a shikaisen lets you change your body as you see fit. Whatever floats the drunk guy boat, I guess, it's not that bad since ZUN just uses Miko as another political chess piece in Gensokyo with the humans vs spiritual beings shit, But I can see how the rabid SJW types latched onto "MUH TRANS RIGHTS MEEKO SHE HATED BEING A MAN AND WANTED TO BE A WOMYN" and ignored everything else about actual Touhou lore.
Honestly he really should have just drawn her as a dude and call it a day, maybe he was just too drunk to think of the consequences of his actions, since he actually can draw men...