I don't think I'd describe Alec as transphobic in general, but he is insanely selfish, and he wants a daughter rather than a son for reasons that have to do with his issues around his twin brother who he murdered, as well as societal sexism and Alec's own preference for women.

He's comfortable using masculinity as a carrot in the whole carrot/stick thing he has going with Isabelle. For her tenth birthday she wanted a suit, and he gave her one; when she's sixteen he takes her hunting; things like that. But at the same time he would never allow a form of gender expression that contradicts his desires. When he wants Isabelle to wear a dress she'll be punished if she tries to wear anything else and medical transition, if Isabelle wanted it, would be completely out of the question. She's his daughter because he wants a daughter, and that's final.

It's worth noting that Alec doesn't know what Isabelle's gender identity actually is, and neither does Isabelle. With my canon taking place somewhere unspecified in the 20th century, both of their knowledge is a little limited, especially Isabelle's. Alec knows that trans people exist but if he had to guess what's going on with Isabelle gender-wise, he'd describe her as a bisexual woman who wants to be butch.