Why is Boruto's Dojutsu different?
Sasuke did not awaken his Rinnegan himself.It was given to him by Hagoromo,he had no such "choice" of awakening only one Rinnegan.It was Hagoromo's decision to give him only one Rinnegan to avoid it's misuse which Madara had done.

Coming to Boruto's Jougan,it's just a very rare case of Byakugan that was triggered probably because of Naruto's enormous chakra.He awakened it only in one eye,not two,the explanation for which is not very clear.