I wouldn't really call this headcanon crazy, but it's one that I'm very fond of: Alphinaud and Alisaie are identical twins. I feel like this is a fairly reasonable assumption to make given their appearance. While it's possible for fraternal twins to look very similar, it's not as likely as it is with identical twins, and Alphinaud and Alisaie look similar to the point that characters in-universe mix them up; however, there's a major detail that throws a wrench in this idea, which is that identical twins are always the same sex. There's an easy explanation to get around this, though. It's one that I'm almost positive wasn't intentional on the writers' part, but that amusingly seems to have some accidental evidence supporting it: one of the twins is trans, and it's probably Alphinaud.

The reason why I headcanon Alphinaud as being trans rather than Alisaie is simply that I think there's a bit more in the text supporting it. He gets mistaken for a girl at a few points. In one instance of this, Matoya immediately assumes he's "Louisoix's granddaughter" upon seeing him as a teenager for the first time. This is probably meant to be her mistaking him for Alisaie, but I think it's fun to interpret this as her either not being aware of Louisoix having a grandson or forgetting that he has one. After all, Alphinaud and Alisaie were taken away from New Sharlayan when they were still infants, so Matoya likely didn't see them at all during the time they were gone and may have not received a ton of information on their status.

Anyway, in this headcanon, I imagine Alphinaud socially transitioned when he was pretty young (before attending the Studium), so him being trans isn't very widely known. Outside of his family, the Scions and some close friends probably know.