I think that it is important to mention that you got drowned by Elizabeths during the baptism process. You can see the priest right before you turn around and see Elizabeth. You can even hear him talking when the Elizabeths are revealing to you, that you are Comstock. Because of that only Comstock-Booker dies, but…

It is because Slate doesn't recognize Comstock as Booker who fought at Wounded Knee.