So, they are the same up until a certain point when you both go different ways, living different lifes and having diverging experiences (as in, not a duplicate of one another), despite looking the same but since the world is big, that doesn`t bat an eye to more than 90% of the population. In that moment I believe you would essentially become two different people (with still its similarities, of course). I believe that because in my view experiences shapes a person further from what is born like. In that sense this Ben is different than the 90`s Ben, because he experienced things the didn`t before thus shaping him the way he seems to be now, rejecting both his former life and the Jackal identity he born for a while.
Basically, if you like it it`s Ben if you don`t it`s just another version. I have no problem viewing them as the same because the end equation is still a clone and still the same memeries and there`s nothing indicating that had 90`s Ben been trapped, tortured and abused further by Warren for years that the same wouldn`t have happen. In my book it`s not a plot point that was made ever impossible before, they just decided to go this route. Another office might have not, who knows.