I think that without being treated as a freak by his own father at least on that count, he would be less likely to act out as much as he did. Also without his father's bad attitude toward Lex because of the storm, Lillian may not have killed Julian or Lionel might have actually believed Lex when he said it was an accident. Also I think being more normal looking might have cut down on the constant bullying.

As for adoption, considering that Bo was constantly in financial trouble even with an unpaid slave on staff aka Clark, I don't think that they could afford the adoption process or that a court wouldn't bug them about why they were constantly on the verge of bankruptcy.