I'd love to discuss the issues of gender identity, but I've never seen the series and I remain true to my own philosophy. When someone's body has boobs, they're female.
I haven't seen the series yet either, but it's clear this is a genderswap, if that really is a guy, evident from the variations of this image. Updated tags.
Okay, I finished the series. Waporif really is a guy. Simoun is interesting in that its characters are all female when they are born, and remain so until they are (usually) forced to choose their sex at age 17. Notably, in real life all humans are female at conception, but males are altered by their Y gene which induces the change in sex. Simoun takes that idea and makes it much more interesting. Great show, it is.
Anyway, I wouldn't really call this a spoiler, as it is just something kind of left ambiguous in the show, but is accepted as true from the get-go. Whatever: Waporif seems to have chosen her sex not too long before the start of the show. The progression from female to male seems to take anywhere from several months to years to complete. That is why "he" still has a respectable rack throughout most of the show. He is shown as a full male at the very end.
I digress. When people are searching the yuri tag they want girl on girl, and I would say Waporif is still very much female at this point.