I think the whole shadow thing only really holds true on one (the rebel) of the three possible paths in your own game. It will certainly make romancing a certain character (Radjack) on that path awkward…to say the least. 
The other two, mage and noble, I think are able to forge a more independent identity of their own, seeing as how they are going to lead the sort of lives the original protagonist could never have, while the Rebel one does go on to kind of fill their predecessors boots, so to speak. Seeing as how the rebel is going to be surrounded by everyone and everything from Flash’s old life. 
In that you have succeeded marvelously I say. 