tbf, the twins' costumes are on Elezen kid bodies, which are pretty formless and don't have defining obvious gender bits so they're easier to mold to fit a body with no booba, and a body with booba. You could swap the hairstyles on Alphinaud and give the head the lip tint and bam, you'd just have Alisaie in his costume, which is probably their thinking (same with Alphi in Alisaie's SB costume; switch the hair on her model, take off the lip tint, and you have Alphinaud instead in her costume.)
Characters that have more defined bodies are probably more "iconic" in their thinking, like the cleavage window on Lyse's red dress, or the halter top and butt window Minfilia's Antecedent attire has. Aymeric's coat is genderlocked to dudes because that's the body type it was modeled for, but the hair is not (imagine spending $18 for hair... couldn't be me... lmao) but it's likely just that: these looks are more defined by who is wearing them, and they don't want to take that away, much like a black mage can't wear white mage AF. Probably those same reasons.