This is one of those instances where I think holding the fact that a woman is only known by her title runs counter to the spirit of the rule. I always understood that rule to avoid arbitrarily passing a movie because a woman orders coffee from an unnamed barista.
It's not as clear cut as, say Dame Judy Dench's turn as M in the James Bond franchise, but if the Moon King, the film's Big Bad, is only ever known by his title, holding that against his daughter seems petty. (Plus, since, as a toy, Monkey was called Mr. Monkey, I think it's fair to call that a name, if an unimaginative one.)
However, I also question that the conversation during the duel on the ship counts as "about something other than a man". The conversation centers around Kubo's mother, but specifically her "betrayal" of her father, marriage to her husband, and protection of her son (and the effect those things had on herself and her sisters).
There is a long conversation between two of the women in the film, during one of the films action sequences. A character falling in love with a man is briefly brought up, but entirely in the context of the female character and her arc, and there is enough conversation preceding this that the conversation would still stand as a conversation if that bit where removed. What keeps this conversation from passing the test is that it is between a named character, Monkey, and one of the two Sisters who are given no names beyond that title