actually in the japanese copy of volume 9 Q&A The whole nonbinary part isn't there, and the author is proposing more of an opinion or guess the literal translation is : "Which gender is Macaron? I supposed you could say... both female and male..."
Why are they surprised at thr fact that Rayne is a three-liners and not that he used summons? Only three-liners can use summon so they should know Rayne is a three-liners since he used summons. Only a few can use summons tho, not every three-liners can.
I think rayne being a three liner is a secret, that's why they were surprised, coupled with the fact that he's the youngest one to ever get it. As for the summons part. I believe they would already suspect that he would have it, since they are divine visionaries. I think they know that some three liners can have summons. Also, the edit you're referring to probably has other things going on, so I can't redirect focus away for it.