That`s where the whole identity crisis theory comes in. Someone having the same first and last name is one thing, that can happen aplenty. Being the same person with the same memories, a duplicate, is another. That one person, being also you, would likely naturally feel equally entitled to live that same life. Maybe it`s just drama for dramas sake but this being a medium that explores the same..
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.