About the first epilogue:
Someone pointed in the Erfworld Forums that the Tool speech somewhat sounds like Wanda's Speech on book one afte being beaten by Ansom.
And the way Isaac reacts after being chastised, not in awe from the Tool, but just speaking like to someone he already knew.
Well, what if Wanda managed to transfer her own string to the Arkentool? After all, she had learned how to deal with strings when fighting Charlie for Lilith, and later used that knowledge to Bind Isaac's string to the Doll. She already had a strong link between her string and the tool on the attunement. If her imminent croaking was fated, as Wanda seemed to be aware, why not take that gamble? It would also allows her to fulfill her fate of serving with Jillian, who is also fated to one day attune with an Arkentool. And it's the convenient way for Wanda to bypass the deal of a lifetime. Also, it links obliquely with the book's overall theme of strings and puppets. Wanda becoming something that will be manipulated by other person.
So, Wanda basically becomes a Soul Reaver. And there's the old annecdote that Wanda is a Chinese Plier manufacturer in our world.
Edit: Oh, yes, and also there's giving sentience to each City's tower. She may have learned a few tricks from that.