BaS certainly is canon.

As for Comstock, the one in Rapture was the last one and he only survived because he left his own reality. The only way to get rid of Comstock was to make sure he never was. Elizabeth: "Dead? You mean like Chen Lin? Like Lady Comstock? No. He is alive in a million million worlds. It's not over because the Prophet is dead. It will only be over when he never even lived in the first place." The only way to make sure there is no Comstock is to kill Booker before he made the choice that birthed Comstock. accepting the baptism.

As for Elizabeth surviving the Last Baptism it is probably because of her powers. She became somewhat like the Luteces. sm