Other than these, according to another theory again the story would track Clem's footsteps and game may start not just after those two shadowy figures find Clem but from a distant point as some time passed or new events may took place on one or two years later, etc...
I personally prefer to come across with Clem in a completely different story which she assuming the key role again. This kind of "Yeeees, I just met this girl but I magically know her past" feeling works much for me playing as a new main character.
(I still prefer Lilly as a protagonist above all possibilities, cause I think it is possible to create a good drama between her and Clem. Think about it, she murdered someone in front of Clem, Clem knew her darkest secret and they are both in a new group. New encounters, new decisions plus a silent past between these two women.
Think about the tension

)