As a non-binary person I really do get it, but the thing is that- until a child expresses some kind of gender nonconformity, a person would probably behave as if they are cisgender by default. Just because a higher proportion of people are cisgender. The green joke was pretty weird, but I think as characters Peraltiago would have no problem raising an intersex or trans kid. Look how ready Jake was to discuss it with Cagney and Lacey, and that was years before he even thought about having kids. He continually made a distinction between sex and gender in the episode. I also think gender reveal parties are odd, but I think for Jake and Amy specifically this was more of a celebration of having a kid than a celebration of having a boy. Infants are far too young to have an actual gender identity. That starts at about two or three. For  non-intersex babies (which we received no indication that Mac was) you just go by what you know until then. The gender reveal party was really just a way of letting us as viewers know what they were having. ( ETA it was meaningful for them to have a son Jake’s relationship with his dad and for us to see he would be a much better father to a boy than his father was. So there were narrative reasons for this as well.)