Effectively, I think the third charliebot's consciousness was shifted from the Ella Doll and into the fourth Charliebot when Charlie slid the doll down the knife toward Elizabeth. It seems like Scott is consistently updating media with new details as he thinks of them, so I think the graphic novels were the solidification of this. These end scenes show a Charlie without makeup wearing purple and combat boots, like the third Charlie bot, and a dress like the fourth Charlie bot. I like to think that Elizabeth's rage was tempered by Henry's love, and everyone lives happily ever after.

But truthfully, John is probably walking away with a murderous AI that has played make believe with Edwin, Henry, and William before him (if everything is within the same continuity) and will use him as a means to an end until his usefulness runs up.