This isn't really a full battle between Madara and Kakashi (I think we know who'd win). But rather a discussion as to whether or not Madara could survive a blast from Kakashi's trans-dimensional MS. I think it WOULD affect Madara.
sure there is weakness.. because if there is not.. why all the uchihas didnt do as himcuz he's able to think.....duh
if he kills everyone, who can he then control