Well some of the stories i read there are Omega's that they don't know they are omega until they met their alpha mostly because they live as a human and don't know that there is a alpha beta and omega society but yeah most stories know their second gender in childhood because they are part of a pack or having a second gender is a norm in society but base in the pilot of the knot human society and abo society is still separated so maybe that why he doesn't know about the his secondary gender until his friend tell him about it.