It's Oro. Mitsuki was probably made in a lab, and Oro contributed some of his DNA, making him the "father." Doesn't have to mean Oro got pregnant, that he's married, or even had ***.
It's like Gargoyles. Thailog has 3 "fathers" Xanatos, Dr. Severeous, and Goliath. All 3 of them contributed to his existence, and thus are thought of as his fathers.
You have Nemu of Bleach. She was created by Mayuri, using his artificial body technique with his artificial soul technique, and threw in his DNA as well. Thus, making Mayuri her father, as she refers to him. And having his DNA, she has similar taste to him as well. But Mayuri is not a woman, didn't get pregnant, and was nowhere close to dating a woman.
You have The Powerpuff Girls. While they rarely call him "dad", the Professor created them, and is referenced to being their father. But the professor was single before that, and only shown dating 2 women-both of which were after the girls came along, and whom the girls tried to set him up with.
It's not a new thing in fiction. We'll probably get a databook explaining it. Until then, best to just say Oro created Mitsuki, rather than rack your brain for other things, like him getting pregnant, or wondering who the mother is.
