Oh, things would be very different if Isabelle was assigned male at birth. Isabelle was born in the midst of Alec's turmoil over his twin brother, Bertrand, and Alec projected a lot of those feelings onto her even with her being seen as a girl. If she'd been a cis boy instead, Alec probably would've been even more repressive, fearing that Isabelle would ultimately kill him the way he killed Bertrand when she was a few months old. I'm genuinely not sure that Isabelle would've survived as a cis boy.

The good news is that if boy!Isabelle did live, Viola wouldn't be so harsh or cruel to him, because he would trigger her trauma less. She would probably still be very distant, but not as hostile. Still, though, overall I think Isabelle would be worse off as Alec's son. As it stands her being genderfluid adds enough complications.